Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge.

PubMed

Bertrand, Erin M; McCrow, John P; Moustafa, Ahmed; Zheng, Hong; McQuaid, Jeffrey B; Delmont, Tom O; Post, Anton F; Sipler, Rachel E; Spackeen, Jenna L; Xu, Kai; Bronk, Deborah A; Hutchins, David A; Allen, Andrew E

2015-08-11

Southern Ocean primary productivity plays a key role in global ocean biogeochemistry and climate. At the Southern Ocean sea ice edge in coastal McMurdo Sound, we observed simultaneous cobalamin and iron limitation of surface water phytoplankton communities in late Austral summer. Cobalamin is produced only by bacteria and archaea, suggesting phytoplankton-bacterial interactions must play a role in this limitation. To characterize these interactions and investigate the molecular basis of multiple nutrient limitation, we examined transitions in global gene expression over short time scales, induced by shifts in micronutrient availability. Diatoms, the dominant primary producers, exhibited transcriptional patterns indicative of co-occurring iron and cobalamin deprivation. The major contributor to cobalamin biosynthesis gene expression was a gammaproteobacterial population, Oceanospirillaceae ASP10-02a. This group also contributed significantly to metagenomic cobalamin biosynthesis gene abundance throughout Southern Ocean surface waters. Oceanospirillaceae ASP10-02a displayed elevated expression of organic matter acquisition and cell surface attachment-related genes, consistent with a mutualistic relationship in which they are dependent on phytoplankton growth to fuel cobalamin production. Separate bacterial groups, including Methylophaga, appeared to rely on phytoplankton for carbon and energy sources, but displayed gene expression patterns consistent with iron and cobalamin deprivation. This suggests they also compete with phytoplankton and are important cobalamin consumers. Expression patterns of siderophore- related genes offer evidence for bacterial influences on iron availability as well. The nature and degree of this episodic colimitation appear to be mediated by a series of phytoplankton-bacterial interactions in both positive and negative feedback loops.

Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge

PubMed Central

Bertrand, Erin M.; McCrow, John P.; Moustafa, Ahmed; Zheng, Hong; McQuaid, Jeffrey B.; Delmont, Tom O.; Post, Anton F.; Sipler, Rachel E.; Spackeen, Jenna L.; Xu, Kai; Bronk, Deborah A.; Hutchins, David A.; Allen, Andrew E.

2015-01-01

Southern Ocean primary productivity plays a key role in global ocean biogeochemistry and climate. At the Southern Ocean sea ice edge in coastal McMurdo Sound, we observed simultaneous cobalamin and iron limitation of surface water phytoplankton communities in late Austral summer. Cobalamin is produced only by bacteria and archaea, suggesting phytoplankton–bacterial interactions must play a role in this limitation. To characterize these interactions and investigate the molecular basis of multiple nutrient limitation, we examined transitions in global gene expression over short time scales, induced by shifts in micronutrient availability. Diatoms, the dominant primary producers, exhibited transcriptional patterns indicative of co-occurring iron and cobalamin deprivation. The major contributor to cobalamin biosynthesis gene expression was a gammaproteobacterial population, Oceanospirillaceae ASP10-02a. This group also contributed significantly to metagenomic cobalamin biosynthesis gene abundance throughout Southern Ocean surface waters. Oceanospirillaceae ASP10-02a displayed elevated expression of organic matter acquisition and cell surface attachment-related genes, consistent with a mutualistic relationship in which they are dependent on phytoplankton growth to fuel cobalamin production. Separate bacterial groups, including Methylophaga, appeared to rely on phytoplankton for carbon and energy sources, but displayed gene expression patterns consistent with iron and cobalamin deprivation. This suggests they also compete with phytoplankton and are important cobalamin consumers. Expression patterns of siderophore- related genes offer evidence for bacterial influences on iron availability as well. The nature and degree of this episodic colimitation appear to be mediated by a series of phytoplankton–bacterial interactions in both positive and negative feedback loops. PMID:26221022

Influence of Calcium in Extracellular DNA Mediated Bacterial Aggregation and Biofilm Formation

PubMed Central

Koop, Leena; Wong, Yie Kuan; Ahmed, Safia; Siddiqui, Khawar Sohail; Manefield, Mike

2014-01-01

Calcium (Ca2+) has an important structural role in guaranteeing the integrity of the outer lipopolysaccharide layer and cell walls of bacterial cells. Extracellular DNA (eDNA) being part of the slimy matrix produced by bacteria promotes biofilm formation through enhanced structural integrity of the matrix. Here, the concurrent role of Ca2+ and eDNA in mediating bacterial aggregation and biofilm formation was studied for the first time using a variety of bacterial strains and the thermodynamics of DNA to Ca2+ binding. It was found that the eDNA concentrations under both planktonic and biofilm growth conditions were different among bacterial strains. Whilst Ca2+ had no influence on eDNA release, presence of eDNA by itself favours bacterial aggregation via attractive acid-base interactions in addition, its binding with Ca2+ at biologically relevant concentrations was shown further increase in bacterial aggregation via cationic bridging. Negative Gibbs free energy (ΔG) values in iTC data confirmed that the interaction between DNA and Ca2+ is thermodynamically favourable and that the binding process is spontaneous and exothermic owing to its highly negative enthalpy. Removal of eDNA through DNase I treatment revealed that Ca2+ alone did not enhance cell aggregation and biofilm formation. This discovery signifies the importance of eDNA and concludes that existence of eDNA on bacterial cell surfaces is a key facilitator in binding of Ca2+ to eDNA thereby mediating bacterial aggregation and biofilm formation. PMID:24651318

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter.

PubMed

Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; McHugh, Theresa A; Dijkstra, Paul; Koch, Benjamin J; Marks, Jane C; Hungate, Bruce A

2017-08-01

Microorganisms perform most decomposition on Earth, mediating carbon (C) loss from ecosystems, and thereby influencing climate. Yet, how variation in the identity and composition of microbial communities influences ecosystem C balance is far from clear. Using quantitative stable isotope probing of DNA, we show how individual bacterial taxa influence soil C cycling following the addition of labile C (glucose). Specifically, we show that increased decomposition of soil C in response to added glucose (positive priming) occurs as a phylogenetically diverse group of taxa, accounting for a large proportion of the bacterial community, shift toward additional soil C use for growth. Our findings suggest that many microbial taxa exhibit C use plasticity, as most taxa altered their use of glucose and soil organic matter depending upon environmental conditions. In contrast, bacteria that exhibit other responses to glucose (reduced growth or reliance on glucose for additional growth) clustered strongly by phylogeny. These results suggest that positive priming is likely the prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the positive priming effect in nature.

Linking soil bacterial biodiversity and soil carbon stability.

PubMed

Mau, Rebecca L; Liu, Cindy M; Aziz, Maliha; Schwartz, Egbert; Dijkstra, Paul; Marks, Jane C; Price, Lance B; Keim, Paul; Hungate, Bruce A

2015-06-01

Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.

Unraveling the Enzymatic Activity of Oxygenated Carbon Nanotubes and Their Application in the Treatment of Bacterial Infections.

PubMed

Wang, Huan; Li, Penghui; Yu, Dongqin; Zhang, Yan; Wang, Zhenzhen; Liu, Chaoqun; Qiu, Hao; Liu, Zhen; Ren, Jinsong; Qu, Xiaogang

2018-05-17

Carbon nanotubes (CNTs) and their derivatives have emerged as a series of efficient biocatalysts to mimic the function of natural enzymes in recent years. However, the unsatisfiable enzymatic efficiency usually limits their practical usage ranging from materials science to biotechnology. Here, for the first time, we present the synthesis of several oxygenated-group-enriched carbon nanotubes (o-CNTs) via a facile but green approach, as well as their usage as high-performance peroxidase mimics for biocatalytic reaction. Exhaustive characterizations of the enzymatic activity of o-CNTs have been provided by exploring the accurate effect of various oxygenated groups on their surface including carbonyl, carboxyl, and hydroxyl groups. Because of the "competitive inhibition" effect among all of these oxygenated groups, the catalytic efficiency of o-CNTs is significantly enhanced by weakening the presence of noncatalytic sites. Furthermore, the admirable enzymatic activity of these o-CNTs has been successfully applied in the treatment of bacterial infections, and the results of both in vitro and in vivo nanozyme-mediated bacterial clearance clearly demonstrate the feasibility of o-CNTs as robust peroxidase mimics to effectively decrease the bacterial viability under physiological conditions. We believe that the present study will not only facilitate the construction of novel efficient nanozymes by rationally adjusting the degree of the "competitive inhibition" effect, but also broaden the biological usage of o-CNT-based nanomaterials via their satisfactory enzymatic activity.

Bacterial floc mediated rapid streamer formation in creeping flows

NASA Astrophysics Data System (ADS)

Hassanpourfard, Mahtab; Nikakhtari, Zahra; Ghosh, Ranajay; Das, Siddhartha; Thundat, Thomas; Kumar, Aloke

2015-11-01

One of the contentious problems regarding the interaction of low Reynolds number (Re << 1) fluid flow with bacterial biomass is the formation of filamentous structures called streamers. Recently, we discovered that streamers can be formed from flow-induced deformation of the pre-formed bacterial flocs over extremely small timescales (less than a second). However, these streamers are different than the ones that mediated by biofilms. To optically probe the inception process of these streamers formation, bacterial flocs were embedded with 200 nm red fluorescent polystyrene beads that served as tracers. We also showed that at their inception the deformation of the flocs is dominated by large recoverable strains indicating significant elasticity. These strains subsequently increase tremendously to produce filamentous streamers. At time scales larger than streamers formation time scale, viscous response was observed from streamers. Finally, rapid clogging of microfluidic devices occurred after these streamers formed.

Host-induced bacterial cell wall decomposition mediates pattern-triggered immunity in Arabidopsis

PubMed Central

Liu, Xiaokun; Grabherr, Heini M; Willmann, Roland; Kolb, Dagmar; Brunner, Frédéric; Bertsche, Ute; Kühner, Daniel; Franz-Wachtel, Mirita; Amin, Bushra; Felix, Georg; Ongena, Marc; Nürnberger, Thorsten; Gust, Andrea A

2014-01-01

Peptidoglycans (PGNs) are immunogenic bacterial surface patterns that trigger immune activation in metazoans and plants. It is generally unknown how complex bacterial structures such as PGNs are perceived by plant pattern recognition receptors (PRRs) and whether host hydrolytic activities facilitate decomposition of bacterial matrices and generation of soluble PRR ligands. Here we show that Arabidopsis thaliana, upon bacterial infection or exposure to microbial patterns, produces a metazoan lysozyme-like hydrolase (lysozyme 1, LYS1). LYS1 activity releases soluble PGN fragments from insoluble bacterial cell walls and cleavage products are able to trigger responses typically associated with plant immunity. Importantly, LYS1 mutant genotypes exhibit super-susceptibility to bacterial infections similar to that observed on PGN receptor mutants. We propose that plants employ hydrolytic activities for the decomposition of complex bacterial structures, and that soluble pattern generation might aid PRR-mediated immune activation in cell layers adjacent to infection sites. DOI: http://dx.doi.org/10.7554/eLife.01990.001 PMID:24957336

Microbially mediated mineral carbonation

NASA Astrophysics Data System (ADS)

Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

2010-12-01

Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

Moxifloxacin susceptibility mediates the relationship between causative organism and clinical outcome in bacterial keratitis.

PubMed

Oldenburg, Catherine E; Lalitha, Prajna; Srinivasan, Muthiah; Manikandan, Palanisamy; Bharathi, M Jayahar; Rajaraman, Revathi; Ravindran, Meenakshi; Mascarenhas, Jeena; Nardone, Natalie; Ray, Kathryn J; Glidden, David V; Acharya, Nisha R; Lietman, Thomas M

2013-02-28

Bacterial keratitis is a sight-threatening infection of the cornea that is one of the leading causes of blindness globally. In this report, we analyze the role of moxifloxacin susceptibility in the relationship between causative organisms and clinical outcome in bacteria keratitis. A mediation analysis is used to assess the role of moxifloxacin susceptibility in the relationship between causative organisms and clinical outcome in bacterial keratitis using data collected in a randomized, controlled trial. In the Steroids for Corneal Ulcers Trial (SCUT), 500 corneal infections were treated with topical moxifloxacin. The outcome of 3-week best spectacle-corrected visual acuity was significantly associated with an organism (Streptococcus pneumoniae, Pseudomonas aeruginosa, etc., P = 0.008). An indirect effects mediation model suggests that MIC accounted for approximately 13% (95% confidence interval, 3%-24%, P = 0.015) of the effect of the organism on 3-week visual acuity. Moxifloxacin mediates the relationship between causative organisms and clinical outcome in bacterial keratitis, and is likely on the causal pathway between the organism and outcome. (ClinicalTrials.gov number, NCT00324168.).

Moxifloxacin Susceptibility Mediates the Relationship between Causative Organism and Clinical Outcome in Bacterial Keratitis

PubMed Central

Oldenburg, Catherine E.; Lalitha, Prajna; Srinivasan, Muthiah; Manikandan, Palanisamy; Bharathi, M. Jayahar; Rajaraman, Revathi; Ravindran, Meenakshi; Mascarenhas, Jeena; Nardone, Natalie; Ray, Kathryn J.; Glidden, David V.; Acharya, Nisha R.; Lietman, Thomas M.

2013-01-01

Purpose. Bacterial keratitis is a sight-threatening infection of the cornea that is one of the leading causes of blindness globally. In this report, we analyze the role of moxifloxacin susceptibility in the relationship between causative organisms and clinical outcome in bacteria keratitis. Methods. A mediation analysis is used to assess the role of moxifloxacin susceptibility in the relationship between causative organisms and clinical outcome in bacterial keratitis using data collected in a randomized, controlled trial. Results. In the Steroids for Corneal Ulcers Trial (SCUT), 500 corneal infections were treated with topical moxifloxacin. The outcome of 3-week best spectacle-corrected visual acuity was significantly associated with an organism (Streptococcus pneumoniae, Pseudomonas aeruginosa, etc., P = 0.008). An indirect effects mediation model suggests that MIC accounted for approximately 13% (95% confidence interval, 3%–24%, P = 0.015) of the effect of the organism on 3-week visual acuity. Conclusions. Moxifloxacin mediates the relationship between causative organisms and clinical outcome in bacterial keratitis, and is likely on the causal pathway between the organism and outcome. (ClinicalTrials.gov number, NCT00324168.) PMID:23385795

Carbon nanotubes as in vivo bacterial probes.

PubMed

Bardhan, Neelkanth M; Ghosh, Debadyuti; Belcher, Angela M

2014-09-17

With the rise in antibiotic-resistant infections, non-invasive sensing of infectious diseases is increasingly important. Optical imaging, although safer and simpler, is less developed than other modalities such as radioimaging, due to low availability of target-specific molecular probes. Here we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F'-positive and F'-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F'-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4 × enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08 × and higher signal amplification ~1.4 × , compared with conventional dyes. We show the probe offers greater ~5.7 × enhancement in imaging of S. aureus infective endocarditis. These biologically functionalized, aqueous-dispersed, actively targeted, modularly tunable SWNT probes offer new avenues for exploration of deeply buried infections.

Carbon nanotubes as in vivo bacterial probes

NASA Astrophysics Data System (ADS)

Bardhan, Neelkanth M.; Ghosh, Debadyuti; Belcher, Angela M.

2014-09-01

With the rise in antibiotic-resistant infections, non-invasive sensing of infectious diseases is increasingly important. Optical imaging, although safer and simpler, is less developed than other modalities such as radioimaging, due to low availability of target-specific molecular probes. Here we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F‧-positive and F‧-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F‧-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4 × enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08 × and higher signal amplification ~1.4 × , compared with conventional dyes. We show the probe offers greater ~5.7 × enhancement in imaging of S. aureus infective endocarditis. These biologically functionalized, aqueous-dispersed, actively targeted, modularly tunable SWNT probes offer new avenues for exploration of deeply buried infections.

Carbon Nanotubes as in vivo Bacterial Probes

PubMed Central

Bardhan, Neelkanth M.; Ghosh, Debadyuti; Belcher, Angela M.

2014-01-01

With the rise in antibiotic-resistant infections, noninvasive sensing of infectious diseases is increasingly important. Optical imaging, while safer and simpler, is less developed than other modalities like radioimaging; due to low availability of target-specific molecular probes. Here, we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F'-positive and F'-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F’-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4× enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08×, and higher signal amplification ~1.4×, compared to conventional dyes. We show the probe offers greater ~5.7× enhancement in imaging of S. aureus infective endocarditis. These biologically-functionalized, aqueous-dispersed, actively-targeted, modularly-tunable SWNT probes offer new avenues for exploration of deeply-buried infections. PMID:25230005

A simple and novel modification of comet assay for determination of bacteriophage mediated bacterial cell lysis.

PubMed

Khairnar, Krishna; Sanmukh, Swapnil; Chandekar, Rajshree; Paunikar, Waman

2014-07-01

The comet assay is the widely used method for in vitro toxicity testing which is also an alternative to the use of animal models for in vivo testing. Since, its inception in 1984 by Ostling and Johansson, it is being modified frequently for a wide range of application. In spite of its wide applicability, unfortunately there is no report of its application in bacteriophages research. In this study, a novel application of comet assay for the detection of bacteriophage mediated bacterial cell lysis was described. The conventional methods in bacteriophage research for studying bacterial lysis by bacteriophages are plaque assay method. It is time consuming, laborious and costly. The lytic activity of bacteriophage devours the bacterial cell which results in the release of bacterial genomic material that gets detected by ethidium bromide staining method by the comet assay protocol. The objective of this study was to compare efficacy of comet assay with different assay used to study phage mediated bacterial lysis. The assay was performed on culture isolates (N=80 studies), modified comet assay appear to have relatively higher sensitivity and specificity than other assay. The results of the study showed that the application of comet assay can be an economical, time saving and less laborious alternative to conventional plaque assay for the detection of bacteriophage mediated bacterial cell lysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity.

PubMed

Rabbi, S M F; Daniel, H; Lockwood, P V; Macdonald, C; Pereg, L; Tighe, M; Wilson, B R; Young, I M

2016-09-12

Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250-2000 μm) and micro-aggregates (53-250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.

Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

PubMed Central

Rabbi, S. M. F.; Daniel, H.; Lockwood, P. V.; Macdonald, C.; Pereg, L.; Tighe, M.; Wilson, B. R.; Young, I. M.

2016-01-01

Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250–2000 μm) and micro-aggregates (53–250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes. PMID:27615807

Photochemical alteration of dissolved organic matter and the subsequent effects on bacterial carbon cycling and diversity.

PubMed

Lønborg, Christian; Nieto-Cid, Mar; Hernando-Morales, Victor; Hernández-Ruiz, Marta; Teira, Eva; Álvarez-Salgado, Xosé Antón

2016-05-01

The impact of solar radiation on dissolved organic matter (DOM) derived from 3 different sources (seawater, eelgrass leaves and river water) and the effect on the bacterial carbon cycling and diversity were investigated. Seawater with DOM from the sources was first either kept in the dark or exposed to sunlight (4 days), after which a bacterial inoculum was added and incubated for 4 additional days. Sunlight exposure reduced the coloured DOM and carbon signals, which was followed by a production of inorganic nutrients. Bacterial carbon cycling was higher in the dark compared with the light treatment in seawater and river samples, while higher levels were found in the sunlight-exposed eelgrass experiment. Sunlight pre-exposure stimulated the bacterial growth efficiency in the seawater experiments, while no impact was found in the other experiments. We suggest that these responses are connected to differences in substrate composition and the production of free radicals. The bacterial community that developed in the dark and sunlight pre-treated samples differed in the seawater and river experiments. Our findings suggest that impact of sunlight exposure on the bacterial carbon transfer and diversity depends on the DOM source and on the sunlight-induced production of inorganic nutrients. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Glycerol as an additional carbon source for bacterial cellulose synthesis

NASA Astrophysics Data System (ADS)

Agustin, Y. E.; Padmawijaya, K. S.; Rixwari, H. F.; Yuniharto, V. A. S.

2018-03-01

Bacterial cellulose, the fermentation result of Acetobacter xylinus can be produced when glycerol was used as an additional carbon source. In this research, bacterial cellulose produced in two different fermentation medium, Hestrin and Scharmm (HS) medium and HS medium with additional MgSO4. Concentration of glycerol that used in this research were 0%; 5%; 10%; and 15% (v/v). The optimum conditions of bacterial cellulose production on each experiment variations determined by characterization of the mechanical properties, including thickness, tensile strength and elongation. Fourier Transform Infra Red Spectroscopy (FTIR) revealed the characterization of bacterial cellulose. Results showed that the growth rate of bacterial cellulose in HS-MgSO4-glycerol medium was faster than in HS-glycerol medium. Increasing concentrations of glycerol will lower the value of tensile strength and elongation. Elongation test showed that the elongation bacterial cellulose (BC) with the addition of 4.95% (v/v) glycerol in the HS-MgSO4 medium is the highest elongation value. The optimum bacterial cellulose production was achieved when 4.95% (v/v) of glycerol added into HS-MgSO4 medium with stress at break of 116.885 MPa and 4.214% elongation.

Association of marine viral and bacterial communities with reference black carbon particles under experimental conditions: an analysis with scanning electron, epifluorescence and confocal laser scanning microscopy.

PubMed

Cattaneo, Raffaela; Rouviere, Christian; Rassoulzadegan, Fereidoun; Weinbauer, Markus G

2010-11-01

Black carbon (BC), the product of incomplete combustion of fossil fuels and biomass, constitutes a significant fraction of the marine organic carbon pool. However, little is known about the possible interactions of BC and marine microorganisms. Here, we report the results of experiments using a standard reference BC material in high concentrations to investigate basic principles of the dynamics of natural bacterial and viral communities with BC particles. We assessed the attachment of viral and bacterial communities using scanning electron, epifluorescence and confocal laser scanning microscopy and shifts in bacterial community composition using 16S rRNA gene denaturing gradient gel electrophoresis (DGGE). In 24-h time-course experiments, BC particles showed a strong potential for absorbing viruses and bacteria. Total viral abundance was reduced, whereas total bacterial abundance was stimulated in the BC treatments. Viral and bacterial abundance on BC particles increased with particle size, whereas the abundances of BC-associated viruses and bacteria per square micrometer surface area decreased significantly with BC particle size. DGGE results suggested that BC has the potential to change bacterial community structure and favour phylotypes related to Glaciecola sp. Our study indicates that BC could influence processes mediated by bacteria and viruses in marine ecosystems. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem.

PubMed

Hao, Yi; Ma, Chuanxin; Zhang, Zetian; Song, Youhong; Cao, Weidong; Guo, Jing; Zhou, Guopeng; Rui, Yukui; Liu, Liming; Xing, Baoshan

2018-01-01

The aim of this study was to compare the toxicity effects of carbon nanomaterials (CNMs), namely fullerene (C 60 ), reduced graphene oxide (rGO) and multi-walled carbon nanotubes (MWCNTs), on a mini-ecosystem of rice grown in a loamy potted soil. We measured plant physiological and biochemical parameters and examined bacterial community composition in the CNMs-treated plant-soil system. After 30 days of exposure, all the three CNMs negatively affected the shoot height and root length of rice, significantly decreased root cortical cells diameter and resulted in shrinkage and deformation of cells, regardless of exposure doses (50 or 500 mg/kg). Additionally, at the high exposure dose of CNM, the concentrations of four phytohormones, including auxin, indoleacetic acid, brassinosteroid and gibberellin acid 4 in rice roots significantly increased as compared to the control. At the high exposure dose of MWCNTs and C 60 , activities of the antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) in roots increased significantly. High-throughput sequencing showed that three typical CNMs had little effect on shifting the predominant soil bacterial species, but the presence of CNMs significantly altered the composition of the bacterial community. Our results indicate that different CNMs indeed resulted in environmental toxicity to rice and soil bacterial community in the rhizosphere and suggest that CNMs themselves and their incorporated products should be reasonably used to control their release/discharge into the environment to prevent their toxic effects on living organisms and the potential risks to food safety. Copyright © 2017 Elsevier Ltd. All rights reserved.

Assessing carbon and nitrogen removal in a novel anoxic-aerobic cyanobacterial-bacterial photobioreactor configuration with enhanced biomass sedimentation.

PubMed

de Godos, I; Vargas, V A; Guzmán, H O; Soto, R; García, B; García, P A; Muñoz, R

2014-09-15

The carbon and nitrogen removal potential of an innovative anoxic-aerobic photobioreactor configuration operated with both internal and external recyclings was evaluated under different cyanobacterial-bacterial sludge residence times (9-31 days) during the treatment of wastewaters with low C/N ratios. Under optimal operating conditions, the two-stage photobioreactor was capable of providing organic carbon and nitrogen removals over 95% and 90%, respectively. The continuous biomass recycling from the settler resulted in the enrichment and predominance of rapidly-settling cyanobacterial-bacterial flocs and effluent suspended solid concentrations lower than 35 mg VSS L(-1). These flocs exhibited sedimentation rates of 0.28-0.42 m h(-1) but sludge volumetric indexes of 333-430 ml/g. The decoupling between the hydraulic retention time and sludge retention time mediated by the external recycling also avoided the washout of nitrifying bacteria and supported process operation at biomass concentrations of 1000-1500 mg VSS L(-1). The addition of additional NaHCO3 to the process overcame the CO2 limitation resulting from the intense competition for inorganic carbon between cyanobacteria and nitrifying bacteria in the photobioreactor, which supported the successful implementation of a nitrification-denitrification process. Unexpectedly, this nitrification-denitrification process occurred both simultaneously in the photobioreactor alone (as a result of the negligible dissolved oxygen concentrations) and sequentially in the two-stage anoxic-aerobic configuration with internal NO3(-)/NO2(-) recycling. Copyright © 2014 Elsevier Ltd. All rights reserved.

Host plant species determines symbiotic bacterial community mediating suppression of plant defenses

USDA-ARS?s Scientific Manuscript database

Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We prev...

Direct detection of various pathogens by loop-mediated isothermal amplification assays on bacterial culture and bacterial colony.

PubMed

Yan, Muxia; Li, Weidong; Zhou, Zhenwen; Peng, Hongxia; Luo, Ziyan; Xu, Ling

2017-01-01

In this work, loop-mediated isothermal amplification based detection assay using bacterial culture and bacterial colony for various common pathogens direct detection had been established, evaluated and further applied. A total of five species of common pathogens and nine detection targets (tlh, tdh and trh for V. Parahaemolyticus, rfbE, stx1 and stx2 for E. coli, oprI for P. aeruginosa, invA for Salmonella and hylA for L. monocytogenes) were performed on bacterial culture and bacterial colony LAMP. To evaluate and optimize this assay, a total of 116 standard strains were included. Then, for each detected targets, 20 random selected strains were applied. Results were determined through both visual observation of the changed color by naked eye and electrophoresis, which increased the accuracy of survey. The minimum adding quantity of each primer had been confirmed, and the optimal amplification was obtained under 65 °C for 45 min with 25 μl reaction volume. The detection limit of bacterial culture LAMP and PCR assay were determined to be 10 2 and 10 4 or 10 5  CFU/reaction, respectively. No false positive amplification was observed when subjecting the bacterial -LAMP assay to 116 reference strains. This was the first report of colony-LAMP and culture-LAMP assay, which had been demonstrated to be a fast, reliable, cost-effective and simple method on detection of various common pathogens. Copyright © 2016 Elsevier Ltd. All rights reserved.

Factors shaping bacterial phylogenetic and functional diversity in coastal waters of the NW Mediterranean Sea

NASA Astrophysics Data System (ADS)

Boras, Julia A.; Vaqué, Dolors; Maynou, Francesc; Sà, Elisabet L.; Weinbauer, Markus G.; Sala, Maria Montserrat

2015-03-01

To evaluate the main factors shaping bacterioplankton phylogenetic and functional diversity in marine coastal waters, we carried out a two-year study based on a monthly sampling in Blanes Bay (NW Mediterranean). We expected the key factors driving bacterial diversity to be (1) temperature and nutrient concentration, together with chlorophyll a concentration as an indicator of phytoplankton biomass and, hence, a carbon source for bacteria (here called bottom-up factors), and (2) top-down pressure (virus- and protist-mediated mortality of bacteria). Phylogenetic diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA. Functional diversity was assessed by using monomeric carbon sources in Biolog EcoPlates and by determining the activity of six extracellular enzymes. Our results indicate that the bacterial phylogenetic and functional diversity in this coastal system is shaped mainly by bottom-up factors. A dendrogram analysis of the DGGE banding patterns revealed three main sample clusters. Two clusters differed significantly in temperature, nitrate and chlorophyll a concentration, and the third was characterized by the highest losses of bacterial production due to viral lysis detected over the whole study period. Protistan grazing had no effect on bacterial functional diversity, since there were no correlations between protist-mediated mortality (PMM) and extracellular enzyme activities, and utilization of only two out of the 31 carbon sources (N-acetyl-D-glucosamine and α-cyclodextrin) was correlated with PMM. In contrast, virus-mediated mortality correlated with changes in the percentage of use of four carbon sources, and also with specific leu-aminopeptidase and β-glucosidase activity. This suggests that viral lysate provides a pool of labile carbon sources, presumably including amino acids and glucose, which may inhibit proteolytic and glucosidic activity. Our results indicate that bottom-up factors play a more important role than

Effect of disinfection upon dissolved organic carbon (DOC) in wastewater: bacterial bioassays.

PubMed

Arana, I; Santorum, P; Muela, A; Barcina, I

2000-08-01

Quantitative and qualitative changes in organic matter content of wastewater effluents attributable to chlorination and ozonation have been analysed using bioassays as well as organic carbon direct measures. Bioassays were carried out using the bacterial populations of wastewater and two Escherichia coli strains as test micro-organisms. Our results indicate that pure strains present some advantages over indigenous bacteria. Although wastewater bacterial populations are better adapted to growth in wastewater, E. coli strains are more sensitive to changes in dissolved organic carbon (DOC) content. Moreover, the use of pure cultures allows estimation of the portion of DOC which can be converted in cell biomass, the assimilable organic carbon (AOC). Finally, the results obtained using prototrophic and the auxotrophic strains of E. coli suggested that ozonation alters the amino acid composition of wastewater while chlorination does not change the quantity nor the quality of the DOC present in effluents.

Microbially mediated carbon mineralization: Geoengineering a carbon-neutral mine

NASA Astrophysics Data System (ADS)

Power, I. M.; McCutcheon, J.; Harrison, A. L.; Wilson, S. A.; Dipple, G. M.; Southam, G.

2013-12-01

Ultramafic and mafic mine tailings are a potentially valuable feedstock for carbon mineralization, affording the mining industry an opportunity to completely offset their carbon emissions. Passive carbon mineralization has previously been documented at the abandoned Clinton Creek asbestos mine, and the active Diavik diamond mine and Mount Keith nickel mine, yet the majority of tailings remain unreacted. Examples of microbe-carbonate interactions at each mine suggest that biological pathways could be harnessed to promote carbon mineralization. In suitable environmental conditions, microbes can mediate geochemical processes to accelerate mineral dissolution, increase the supply of carbon dioxide (CO2), and induce carbonate precipitation, all of which may accelerate carbon mineralization. Tailings mineralogy and the availability of a CO2 point source are key considerations in designing tailings storage facilities (TSF) for optimizing carbon mineralization. We evaluate the efficacy of acceleration strategies including bioleaching, biologically induced carbonate precipitation, and heterotrophic oxidation of waste organics, as well as abiotic strategies including enhancing passive carbonation through modifying tailings management practices and use of CO2 point sources (Fig. 1). With the aim of developing carbon-neutral mines, implementation of carbon mineralization strategies into TSF design will be driven by economic incentives and public pressure for environmental sustainability in the mining industry. Figure 1. Schematic illustrating geoengineered scenarios for carbon mineralization of ultramafic mine tailings. Scenarios A and B are based on non-point and point sources of CO2, respectively.

Identification of bacterial contaminants from calcium carbonate filler production lines and an evaluation of biocide based decontamination procedures.

PubMed

Odić, Duško; Prah, Jana; Avguštin, Gorazd

2017-04-01

The aim of this study was to analyze the bacterial community in the production line of a calcium carbonate filler production company and to investigate possible causes for bacterial presence. Throughout 2012, 24 carbonate slurry and six groundwater samples were analyzed. Pseudomonas and Microbacterium were the most frequent contaminants in the slurry, whereas Pseudomonas and Brevundimonas dominated the groundwater samples. Of the 43 different bacterial strains isolated, only five were found both in the slurry and the groundwater, indicating that the latter was not a major source of contamination. The efficacy of 54 commercial biocidal formulations was tested against an artificial bacterial consortium composed of selected slurry isolates. A formulation containing 7.5-15% (v v -1 ) bronopol and 1.0-2.5% (v v -1 ) [chloroisothiazolinone (CIT) + methylisothiazolinone (MIT)] exhibited the highest efficacy. Of the possible causes for bacterial presence, sporogenesis and biocide adsorption to carbonate particles were found to be less probable compared to bacterial adsorption to particles, and the acquisition of resistance to biocides.

Involvement of β-carbonic anhydrase (β-CA) genes in bacterial genomic islands and horizontal transfer to protists.

PubMed

Zolfaghari Emameh, Reza; Barker, Harlan R; Hytönen, Vesa P; Parkkila, Seppo

2018-05-25

Genomic islands (GIs) are a type of mobile genetic element (MGE) that are present in bacterial chromosomes. They consist of a cluster of genes which produce proteins that contribute to a variety of functions, including, but not limited to, regulation of cell metabolism, anti-microbial resistance, pathogenicity, virulence, and resistance to heavy metals. The genes carried in MGEs can be used as a trait reservoir in times of adversity. Transfer of genes using MGEs, occurring outside of reproduction, is called horizontal gene transfer (HGT). Previous literature has shown that numerous HGT events have occurred through endosymbiosis between prokaryotes and eukaryotes.Beta carbonic anhydrase (β-CA) enzymes play a critical role in the biochemical pathways of many prokaryotes and eukaryotes. We have previously suggested horizontal transfer of β-CA genes from plasmids of some prokaryotic endosymbionts to their protozoan hosts. In this study, we set out to identify β-CA genes that might have transferred between prokaryotic and protist species through HGT in GIs. Therefore, we investigated prokaryotic chromosomes containing β-CA-encoding GIs and utilized multiple bioinformatics tools to reveal the distinct movements of β-CA genes among a wide variety of organisms. Our results identify the presence of β-CA genes in GIs of several medically and industrially relevant bacterial species, and phylogenetic analyses reveal multiple cases of likely horizontal transfer of β-CA genes from GIs of ancestral prokaryotes to protists. IMPORTANCE The evolutionary process is mediated by mobile genetic elements (MGEs), such as genomic islands (GIs). A gene or set of genes in the GIs are exchanged between and within various species through horizontal gene transfer (HGT). Based on the crucial role that GIs can play in bacterial survival and proliferation, they were introduced as the environmental- and pathogen-associated factors. Carbonic anhydrases (CAs) are involved in many critical

Impedimetric biosensor based on cell-mediated bioimprinted films for bacterial detection.

PubMed

Qi, Peng; Wan, Yi; Zhang, Dun

2013-01-15

This work presents the synthesis of bacteria-mediated bioimprinted films for selective bacterial detection. Marine pathogen sulfate-reducing bacteria (SRB) were chosen as the template bacteria. Chitosan (CS) doped with reduced graphene sheets (RGSs) was electrodeposited on an indium tin oxide electrode, and the resulting RGSs-CS hybrid film served as a platform for bacterial attachment. The electrodeposition conditions were optimized to obtain RGSs-CS hybrid films with excellent electrochemical performance. A layer of nonconductive CS film was deposited to embed the pathogen, and acetone was used to wash away the bacterial templates. Electrochemical impedance spectroscopy was performed to characterize the stepwise modification process and monitor the SRB population. Faradic impedance measurements revealed that the charge transfer resistance (R(ct)) increased with increased SRB concentration. A linear relationship between ΔR(ct) and the logarithm of SRB concentration was obtained within the concentration range of 1.0×10(4)cfum L(-1) to 1.0×10(8)cfum L(-1). The impedimetric sensor showed good selectivity towards SRB based on size and shape. Hence, selectivity for bacterial detection can be improved if the bioimprinting technique is combined with other bio-recognition elements. Copyright © 2012 Elsevier B.V. All rights reserved.

Bacterial community transcription patterns during a marine phytoplankton bloom.

PubMed

Rinta-Kanto, Johanna M; Sun, Shulei; Sharma, Shalabh; Kiene, Ronald P; Moran, Mary Ann

2012-01-01

Bacterioplankton consume a large proportion of photosynthetically fixed carbon in the ocean and control its biogeochemical fate. We used an experimental metatranscriptomics approach to compare bacterial activities that route energy and nutrients during a phytoplankton bloom compared with non-bloom conditions. mRNAs were sequenced from duplicate bloom and control microcosms 1 day after a phytoplankton biomass peak, and transcript copies per litre of seawater were calculated using an internal mRNA standard. Transcriptome analysis revealed a potential novel mechanism for enhanced efficiency during carbon-limited growth, mediated through membrane-bound pyrophosphatases [V-type H(+)-translocating; hppA]; bloom bacterioplankton participated less in this metabolic energy scavenging than non-bloom bacterioplankton, with possible implications for differences in growth yields on organic substrates. Bloom bacterioplankton transcribed more copies of genes predicted to increase cell surface adhesiveness, mediated by changes in bacterial signalling molecules related to biofilm formation and motility; these may be important in microbial aggregate formation. Bloom bacterioplankton also transcribed more copies of genes for organic acid utilization, suggesting an increased importance of this compound class in the bioreactive organic matter released during phytoplankton blooms. Transcription patterns were surprisingly faithful within a taxon regardless of treatment, suggesting that phylogeny broadly predicts the ecological roles of bacterial groups across 'boom' and 'bust' environmental backgrounds. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Carbon utilization profiles of river bacterial strains facing sole carbon sources suggest metabolic interactions.

PubMed

Goetghebuer, Lise; Servais, Pierre; George, Isabelle F

2017-05-01

Microbial communities play a key role in water self-purification. They are primary drivers of biogenic element cycles and ecosystem processes. However, these communities remain largely uncharacterized. In order to understand the diversity-heterotrophic activity relationship facing sole carbon sources, we assembled a synthetic community composed of 20 'typical' freshwater bacterial species mainly isolated from the Zenne River (Belgium). The carbon source utilization profiles of each individual strain and of the mixed community were measured in Biolog Phenotype MicroArrays PM1 and PM2A microplates that allowed testing 190 different carbon sources. Our results strongly suggest interactions occurring between our planktonic strains as our synthetic community showed metabolic properties that were not displayed by its single components. Finally, the catabolic performances of the synthetic community and a natural community from the same sampling site were compared. The synthetic community behaved like the natural one and was therefore representative of the latter in regard to carbon source consumption. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems.

PubMed

Lynn, Tin Mar; Ge, Tida; Yuan, Hongzhao; Wei, Xiaomeng; Wu, Xiaohong; Xiao, Keqing; Kumaresan, Deepak; Yu, San San; Wu, Jinshui; Whiteley, Andrew S

2017-04-01

CO 2 assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of 14 C ( 14 C-MBC) differed among the soils from three ecosystems, accounting for 14.2-20.2% of 14 C-labeled soil organic carbon ( 14 C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, 14 C-SOC level, and 14 C-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO 2 -fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.

Effects of ultrasonic pretreatment on quantity and composition of bacterial DNA recovered from granular activated carbon used for drinking water treatment.

PubMed

Kim, Tae Gwan; Kim, Sun-Hye; Cho, Kyung-Suk

2014-01-01

Effects of ultrasonic pretreatment on bacterial DNA recovery from granular activated carbon (GAC) were investigated. GAC (Calgon F400), biologically activated, was sampled from an actual drinking water plant. Different ultrasonic energy densities (0-400 J·cm(-3)) were applied with agitation (250 rpm for 30 min), and recovered bacterial DNA was quantified using quantitative PCR. Energy density was linearly correlated with the concentration of carbon fines produced from GAC during ultrasonication. Ultrasonication alone had no effect on DNA recovery at ≤60 J·cm(-3), but a strongly adverse effect at >67 J·cm(-3) due to the produced carbon fines. Agitation along with ultrasonication strongly enhanced the bacterial DNA recovery when ≤40 J·cm(-3) was applied, although it did not affect the production of carbon fines. Ribosomal tag pyrosequencing was used to compare recovered bacterial communities (0, 20 and 30 J·cm(-3) with or without agitation). Ultrasonication allowed for obtaining a more diverse and richer bacterial community from GAC, compared with the control. Agitation did not show a positive effect on community organization (richness and diversity). Consistently, canonical correspondence analysis indicated that the energy density was associated with the relative abundances of particular bacterial members (P < 0.05), while agitation did not. Correspondence analysis revealed that the recovered bacterial communities were grouped according to the applied energy densities. In conclusion, ultrasonication and agitation influence the recovered DNA in quality and quantity, respectively, and carbon fines as a by-product by ultrasonication interfere with the DNA recovery.

Airborne bacterial assemblage in a zero carbon building: A case study.

PubMed

Leung, M H Y; Tong, X; Tong, J C K; Lee, P K H

2018-01-01

Currently, there is little information pertaining to the airborne bacterial communities of green buildings. In this case study, the air bacterial community of a zero carbon building (ZCB) in Hong Kong was characterized by targeting the bacterial 16S rRNA gene. Bacteria associated with the outdoor environment dominated the indoor airborne bacterial assemblage, with a modest contribution from bacteria associated with human skin. Differences in overall community diversity, membership, and composition associated with short (day-to-day) and long-term temporal properties were detected, which may have been driven by specific environmental genera and taxa. Furthermore, time-decay relationships in community membership (based on unweighted UniFrac distances) and composition (based on weighted UniFrac distances) differed depending on the season and sampling location. A Bayesian source-tracking approach further supported the importance of adjacent outdoor air bacterial assemblage in sourcing the ZCB indoor bioaerosol. Despite the unique building attributes, the ZCB microbial assemblage detected and its temporal characteristics were not dissimilar to that of conventional built environments investigated previously. Future controlled experiments and microbial assemblage investigations of other ZCBs will undoubtedly uncover additional knowledge related to how airborne bacteria in green buildings may be influenced by their distinctive architectural attributes. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Carbon fixation in sediments of Sino-Pacific seas-differential contributions of bacterial and archaeal domains

NASA Astrophysics Data System (ADS)

Das, Anindita; Cao, Wenrui; Zhang, Hongjie; Saren, Gaowa; Jiang, Mingyu; Yu, Xinke

2017-11-01

Oceanic stretches experiencing perpetual darkness and extreme limitation of utilizable organic matter often rely on chemosynthetic carbon (C)-fixation. However, C-fixation is not limited to carbon-deplete environments alone but might also occur in varying degrees in carbon-replete locales depending on the nature and concentration of utilizable carbon, electron donors and acceptors. Quantification of microbial C-fixation and relative contribution of domains bacteria and archaea are therefore crucial. The present experiment estimates the differential rates of C-fixation by archaea and bacteria along with the effects of different electron donors. Four Sino-Pacific marine sediments from Bashi strait (Western Pacific Warm Pool), East China Sea, South China Sea and Okinawa Trough were examined. Total microbial C-uptake was estimated by doping of aqueous NaH14CO3. Total bacterial C-uptake was measured by blocking archaeal metabolism using inhibitor GC7. Archaeal contribution was estimated by subtracting total bacterial from total microbial C-uptake. Effect of electron donor addition was analyzed by spiking with ammonium, sulfide, and reduced metals. Results suggested that C-fixation in marine sediments was not the function of archaea alone, which was in contrast to results from several recent publications. C-fixing bacteria are also equally active. Often in spite of great effort of one domain to fix carbon, the system does not become net C-fixing due to equal and opposite C-releasing activity of the other domain. Thus a C-releasing bacterial or archaeal community can become C-fixing with the change of nature and concentration of electron donors.

Arsenic uptake in bacterial calcite

NASA Astrophysics Data System (ADS)

Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

2018-02-01

Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and X-ray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03 Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

L-arginine mediated renaturation enhances yield of human, α6 type IV collagen non-collagenous domain from bacterial inclusion bodies

PubMed Central

Gunda, Venugopal; Boosani, Chandra Shekhar; Verma, Raj Kumar; Guda, Chittibabu; Akul Sudhakar, Yakkanti

2012-01-01

The anti-angiogenic, carboxy terminal non-collagenous domain (NC1) derived from human Collagen type IV alpha 6 chain, [α6(IV)NC1] or hexastatin, was earlier obtained using different recombinant methods of expression in bacterial systems. However, the effect of L-arginine mediated renaturation in enhancing the relative yields of this protein from bacterial inclusion bodies has not been evaluated. In the present study, direct stirring and on-column renaturation methods using L-arginine and different size exclusion chromatography matrices were applied for enhancing the solubility in purifying the recombinant α6(IV)NC1 from bacterial inclusion bodies. This methodology enabled purification of higher quantities of soluble protein from inclusion bodies, which inhibited endothelial cell proliferation, migration and tube formation. Thus, the scope for L-arginine mediated renaturation in obtaining higher yields of soluble, biologically active NC1 domain from bacterial inclusion bodies was evaluated. PMID:22512648

L-arginine mediated renaturation enhances yield of human, α6 Type IV collagen non-collagenous domain from bacterial inclusion bodies.

PubMed

Gunda, Venugopal; Boosani, Chandra Shekhar; Verma, Raj Kumar; Guda, Chittibabu; Sudhakar, Yakkanti Akul

2012-10-01

The anti-angiogenic, carboxy terminal non-collagenous domain (NC1) derived from human Collagen type IV alpha 6 chain, [α6(IV)NC1] or hexastatin, was earlier obtained using different recombinant methods of expression in bacterial systems. However, the effect of L-arginine mediated renaturation in enhancing the relative yields of this protein from bacterial inclusion bodies has not been evaluated. In the present study, direct stirring and on-column renaturation methods using L-arginine and different size exclusion chromatography matrices were applied for enhancing the solubility in purifying the recombinant α6(IV)NC1 from bacterial inclusion bodies. This methodology enabled purification of higher quantities of soluble protein from inclusion bodies, which inhibited endothelial cell proliferation, migration and tube formation. Thus, the scope for L-arginine mediated renaturation in obtaining higher yields of soluble, biologically active NC1 domain from bacterial inclusion bodies was evaluated.

Sink or link? The bacterial role in benthic carbon cycling in the Arabian Sea's oxygen minimum zone

NASA Astrophysics Data System (ADS)

Pozzato, L.; Van Oevelen, D.; Moodley, L.; Soetaert, K.; Middelburg, J. J.

2013-11-01

The bacterial loop, the consumption of dissolved organic matter (DOM) by bacteria and subsequent transfer of bacterial carbon to higher trophic levels, plays a prominent role in pelagic food webs. However, its role in sedimentary ecosystems is not well documented. Here we present the results of isotope tracer experiments performed under in situ oxygen conditions in sediments from inside and outside the Arabian Sea's oxygen minimum zone (OMZ) to study the importance of the microbial loop in this setting. Particulate organic matter, added as phytodetritus, was processed by bacteria, protozoa and metazoans, while dissolved organic matter was processed only by bacteria and there was very little, if any, transfer to higher trophic levels within the 7 day experimental period. This lack of significant transfer of bacterial-derived carbon to metazoan consumers indicates that the bacterial loop is rather inefficient, in sediments both inside and outside the OMZ. Moreover, metazoans directly consumed labile particulate organic matter resources and thus competed with bacteria for phytodetritus.

Sink or link? The bacterial role in benthic carbon cycling in the Arabian sea oxygen minimum zone

NASA Astrophysics Data System (ADS)

Pozzato, L.; Van Oevelen, D.; Moodley, L.; Soetaert, K.; Middelburg, J. J.

2013-06-01

The bacterial loop, the consumption of dissolved organic matter (DOM) by bacteria and subsequent transfer of bacterial carbon to higher trophic levels, plays a prominent role in pelagic aquatic food webs. However, its role in sedimentary ecosystems is not well documented. Here we present the results of isotope tracer experiments performed under in situ oxygen conditions in sediments from inside and outside the Arabian Sea Oxygen Minimum Zone (OMZ) to study the importance of the microbial loop in this setting. Particulate organic matter, added as phytodetritus, was processed by bacteria, protozoa and metazoans, while dissolved organic matter was processed only by bacteria and there was very little, if any, transfer to higher trophic levels within the experimental period. This lack of significant transfer of bacterial-derived carbon to metazoan consumers indicates that the bacterial loop is rather inefficient in these sediments. Moreover, metazoans directly consume labile particulate organic matter resources and thus compete with bacteria for phytodetritus.

Adsorption and oxidation of SO₂in a fixed-bed reactor using activated carbon produced from oxytetracycline bacterial residue and impregnated with copper.

PubMed

Zhou, Baohua; Yu, Lei; Song, Hanning; Li, Yaqi; Zhang, Peng; Guo, Bin; Duan, Erhong

2015-02-01

The SO₂removal ability (including adsorption and oxidation ability) of activated carbon produced from oxytetracycline bacterial residue and impregnated with copper was investigated. The activated carbon produced from oxytetracycline bacterial residue and modified with copper was characterized by x-ray diffraction, scanning electron microscopy, and energy-dispersive spectroscopy. The effects of the catalysts, SO₂concentration, weight hourly space velocity, and temperature on the SO₂adsorption and oxidation activity were evaluated. Activated carbon produced from oxytetracycline bacterial residue and used as catalyst supports for copper oxide catalysts provided high catalytic activity for the adsorbing and oxidizing of SO₂from flue gases.

Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks

PubMed Central

Bourqui, Romain; Benchimol, William; Gaspin, Christine; Sirand-Pugnet, Pascal; Uricaru, Raluca; Dutour, Isabelle

2015-01-01

The revolution in high-throughput sequencing technologies has enabled the acquisition of gigabytes of RNA sequences in many different conditions and has highlighted an unexpected number of small RNAs (sRNAs) in bacteria. Ongoing exploitation of these data enables numerous applications for investigating bacterial transacting sRNA-mediated regulation networks. Focusing on sRNAs that regulate mRNA translation in trans, recent works have noted several sRNA-based regulatory pathways that are essential for key cellular processes. Although the number of known bacterial sRNAs is increasing, the experimental validation of their interactions with mRNA targets remains challenging and involves expensive and time-consuming experimental strategies. Hence, bioinformatics is crucial for selecting and prioritizing candidates before designing any experimental work. However, current software for target prediction produces a prohibitive number of candidates because of the lack of biological knowledge regarding the rules governing sRNA–mRNA interactions. Therefore, there is a real need to develop new approaches to help biologists focus on the most promising predicted sRNA–mRNA interactions. In this perspective, this review aims at presenting the advantages of mixing bioinformatics and visualization approaches for analyzing predicted sRNA-mediated regulatory bacterial networks. PMID:25477348

Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks.

PubMed

Thébault, Patricia; Bourqui, Romain; Benchimol, William; Gaspin, Christine; Sirand-Pugnet, Pascal; Uricaru, Raluca; Dutour, Isabelle

2015-09-01

The revolution in high-throughput sequencing technologies has enabled the acquisition of gigabytes of RNA sequences in many different conditions and has highlighted an unexpected number of small RNAs (sRNAs) in bacteria. Ongoing exploitation of these data enables numerous applications for investigating bacterial transacting sRNA-mediated regulation networks. Focusing on sRNAs that regulate mRNA translation in trans, recent works have noted several sRNA-based regulatory pathways that are essential for key cellular processes. Although the number of known bacterial sRNAs is increasing, the experimental validation of their interactions with mRNA targets remains challenging and involves expensive and time-consuming experimental strategies. Hence, bioinformatics is crucial for selecting and prioritizing candidates before designing any experimental work. However, current software for target prediction produces a prohibitive number of candidates because of the lack of biological knowledge regarding the rules governing sRNA-mRNA interactions. Therefore, there is a real need to develop new approaches to help biologists focus on the most promising predicted sRNA-mRNA interactions. In this perspective, this review aims at presenting the advantages of mixing bioinformatics and visualization approaches for analyzing predicted sRNA-mediated regulatory bacterial networks. © The Author 2014. Published by Oxford University Press.

The antigen 43 structure reveals a molecular Velcro-like mechanism of autotransporter-mediated bacterial clumping

PubMed Central

Heras, Begoña; Totsika, Makrina; Peters, Kate M.; Paxman, Jason J.; Gee, Christine L.; Jarrott, Russell J.; Perugini, Matthew A.; Whitten, Andrew E.; Schembri, Mark A.

2014-01-01

Aggregation and biofilm formation are critical mechanisms for bacterial resistance to host immune factors and antibiotics. Autotransporter (AT) proteins, which represent the largest group of outer-membrane and secreted proteins in Gram-negative bacteria, contribute significantly to these phenotypes. Despite their abundance and role in bacterial pathogenesis, most AT proteins have not been structurally characterized, and there is a paucity of detailed information with regard to their mode of action. Here we report the structure–function relationships of Antigen 43 (Ag43a), a prototypic self-associating AT protein from uropathogenic Escherichia coli. The functional domain of Ag43a displays a twisted L-shaped β-helical structure firmly stabilized by a 3D hydrogen-bonded scaffold. Notably, the distinctive Ag43a L shape facilitates self-association and cell aggregation. Combining all our data, we define a molecular “Velcro-like” mechanism of AT-mediated bacterial clumping, which can be tailored to fit different bacterial lifestyles such as the formation of biofilms. PMID:24335802

Consolidation of archaeological gypsum plaster by bacterial biomineralization of calcium carbonate.

PubMed

Jroundi, Fadwa; Gonzalez-Muñoz, Maria Teresa; Garcia-Bueno, Ana; Rodriguez-Navarro, Carlos

2014-09-01

Gypsum plasterworks and decorative surfaces are easily degraded, especially when exposed to humidity, and thus they require protection and/or consolidation. However, the conservation of historical gypsum-based structural and decorative materials by conventional organic and inorganic consolidants shows limited efficacy. Here, a new method based on the bioconsolidation capacity of carbonatogenic bacteria inhabiting the material was assayed on historical gypsum plasters and compared with conventional consolidation treatments (ethyl silicate; methylacrylate-ethylmethacrylate copolymer and polyvinyl butyral). Conventional products do not reach in-depth consolidation, typically forming a thin impervious surface layer which blocks pores. In contrast, the bacterial treatment produces vaterite (CaCO3) biocement, which does not block pores and produces a good level of consolidation, both at the surface and in-depth, as shown by drilling resistance measurement system analyses. Transmission electron microscopy analyses show that bacterial vaterite cement formed via oriented aggregation of CaCO3 nanoparticles (∼20nm in size), resulting in mesocrystals which incorporate bacterial biopolymers. Such a biocomposite has superior mechanical properties, thus explaining the fact that drilling resistance of bioconsolidated gypsum plasters is within the range of inorganic calcite materials of equivalent porosity, despite the fact that the bacterial vaterite cement accounts for only a 0.02 solid volume fraction. Bacterial bioconsolidation is proposed for the effective consolidation of this type of material. The potential applications of bacterial calcium carbonate consolidation of gypsum biomaterials used as bone graft substitutes are discussed. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

M-CSF Mediates Host Defense during Bacterial Pneumonia by Promoting the Survival of Lung and Liver Mononuclear Phagocytes.

PubMed

Bettina, Alexandra; Zhang, Zhimin; Michels, Kathryn; Cagnina, R Elaine; Vincent, Isaah S; Burdick, Marie D; Kadl, Alexandra; Mehrad, Borna

2016-06-15

Gram-negative bacterial pneumonia is a common and dangerous infection with diminishing treatment options due to increasing antibiotic resistance among causal pathogens. The mononuclear phagocyte system is a heterogeneous group of leukocytes composed of tissue-resident macrophages, dendritic cells, and monocyte-derived cells that are critical in defense against pneumonia, but mechanisms that regulate their maintenance and function during infection are poorly defined. M-CSF has myriad effects on mononuclear phagocytes but its role in pneumonia is unknown. We therefore tested the hypothesis that M-CSF is required for mononuclear phagocyte-mediated host defenses during bacterial pneumonia in a murine model of infection. Genetic deletion or immunoneutralization of M-CSF resulted in reduced survival, increased bacterial burden, and greater lung injury. M-CSF was necessary for the expansion of lung mononuclear phagocytes during infection but did not affect the number of bone marrow or blood monocytes, proliferation of precursors, or recruitment of leukocytes to the lungs. In contrast, M-CSF was essential to survival and antimicrobial functions of both lung and liver mononuclear phagocytes during pneumonia, and its absence resulted in bacterial dissemination to the liver and hepatic necrosis. We conclude that M-CSF is critical to host defenses against bacterial pneumonia by mediating survival and antimicrobial functions of mononuclear phagocytes in the lungs and liver. Copyright © 2016 by The American Association of Immunologists, Inc.

M-CSF mediates host defense during bacterial pneumonia by promoting the survival of lung and liver mononuclear phagocytes

PubMed Central

Bettina, Alexandra; Zhang, Zhimin; Michels, Kathryn; Cagnina, R. Elaine; Vincent, Isaah S.; Burdick, Marie D.; Kadl, Alexandra; Mehrad, Borna

2016-01-01

Gram-negative bacterial pneumonia is a common and dangerous infection with diminishing treatment options due to increasing antibiotic resistance among causal pathogens. The mononuclear phagocyte system is a heterogeneous group of leukocytes composed of tissue-resident macrophages, dendritic cells and monocyte-derived cells that are critical in defense against pneumonia, but mechanisms that regulate their maintenance and function during infection are poorly defined. Macrophage-colony stimulating factor (M-CSF) has myriad effects on mononuclear phagocytes but its role in pneumonia is unknown. We therefore tested the hypothesis that M-CSF is required for mononuclear phagocyte-mediated host defenses during bacterial pneumonia in a murine model of infection. Genetic deletion or immunoneutralization of M-CSF resulted in reduced survival, increased bacterial burden and greater lung injury. M-CSF was necessary for the expansion of lung mononuclear phagocytes during infection but did not affect the number of bone marrow or blood monocytes, the proliferation of precursors or the recruitment of leukocytes to the lungs. In contrast, M-CSF was essential to survival and anti-microbial functions of both lung and liver mononuclear phagocytes during pneumonia and its absence resulted in bacterial dissemination to the liver and hepatic necrosis. We conclude that M-CSF is critical to host defenses against bacterial pneumonia by mediating survival and anti-microbial functions of mononuclear phagocytes in the lungs and liver. PMID:27183631

Bacterial Community Structure Shifted by Geosmin in Granular Activated Carbon System of Water Treatment Plants.

PubMed

Pham, Ngoc Dung; Lee, Eun-Hee; Chae, Seon-Ha; Cho, Yongdeok; Shin, Hyejin; Son, Ahjeong

2016-01-01

We investigated the relation between the presence of geosmin in water and the bacterial community structure within the granular activated carbon (GAC) system of water treatment plants in South Korea. GAC samples were collected in May and August of 2014 at three water treatment plants (Sungnam, Koyang, and Yeoncho in Korea). Dissolved organic carbon and geosmin were analyzed before and after GAC treatment. Geosmin was found in raw water from Sungnam and Koyang water treatment plants but not in that from Yeoncho water treatment plant. Interestingly, but not surprisingly, the 16S rRNA clone library indicated that the bacterial communities from the Sungnam and Koyang GAC systems were closely related to geosmin-degrading bacteria. Based on the phylogenetic tree and multidimensional scaling plot, bacterial clones from GAC under the influence of geosmin were clustered with Variovorax paradoxus strain DB 9b and Comamonas sp. DB mg. In other words, the presence of geosmin in water might have inevitably contributed to the growth of geosmin degraders within the respective GAC system.

Arsenic uptake in bacterial calcite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco

Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and Xray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the cmore » axis (by 0.03Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.« less

Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling

PubMed Central

Sun, Feifei; Zhang, Xiaoli; Zhang, Qianqian; Liu, Fanghua

2015-01-01

Seagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. The nifH phylotypes detected were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa, and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (Deltaproteobacteria) and Anaerolineae (Chloroflexi) presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem. PMID:26209674

Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling.

PubMed

Sun, Feifei; Zhang, Xiaoli; Zhang, Qianqian; Liu, Fanghua; Zhang, Jianping; Gong, Jun

2015-10-01

Seagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. The nifH phylotypes detected were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa, and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (Deltaproteobacteria) and Anaerolineae (Chloroflexi) presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem. Copyright © 2015

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

PubMed Central

Weedon, James T.; Kowalchuk, George A.; Aerts, Rien; Freriks, Stef; Röling, Wilfred F. M.; van Bodegom, Peter M.

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts. PMID:28326062

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland.

PubMed

Weedon, James T; Kowalchuk, George A; Aerts, Rien; Freriks, Stef; Röling, Wilfred F M; van Bodegom, Peter M

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50-100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12-15% of variance explained) > temporal variation (7-11%) > climate treatment (4-9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates-evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

Influence of Three Contrasting Detrital Carbon Sources on Planktonic Bacterial Metabolism in a Mesotrophic Lake.

PubMed

Wehr; Petersen; Findlay

1999-01-01

Abstract Lakes receive organic carbon from a diversity of sources which vary in their contribution to planktonic microbial food webs. We conducted a mesocosm study to test the effects of three different detrital carbon sources (algae, aquatic macrophytes, terrestrial leaves) on several measures of microbial metabolism in a small meso-eutrophic lake (DOC approximately 5 mg/L). Small DOC additions (DeltaC < 1 mg/L) affected bacterial numbers, growth, and pathways of carbon acquisition. Macrophyte and leaf detritus significantly increased TDP and color, but bacterial densities initially (+12 h) were unaffected. After 168 h, densities in systems amended with terrestrial detritus were 60% less than in controls, while production rates in mesocosms with macrophyte detritus were 4-fold greater. Detritus treatments resulted in greater per-cell production rates either through stable cell numbers and greater growth rates (macrophyte-C) or lower densities with stable production rates (terrestrial-C). After only 12 h, rates of leucine aminopeptidase (LAPase) activity were 2.5x greater in macrophyte-C systems than in controls, but LAPase and beta-N-acetylglucosamindase activities in systems amended with terrestrial-C were only 50% of rates in controls. After 168 h, beta-xylosidase rates were significantly greater in communities with terrestrial and phytoplankton detritus. Microbial utilization of >20% of 102 carbon sources tested were affected by at least one detritus addition. Macrophyte-C had positive (6% of substrates) and negative (14%) effects on substrate use; terrestrial detritus had mainly positive effects. An ordination based on carbon-use profiles (+12 h) revealed a cluster of macrophyte-amended communities with greater use of psicose, lactulose, and succinamic acid; controls and algal-detritus systems were more effective in metabolizing two common sugars and cellobiose. After 168 h, communities receiving terrestrial detritus were most tightly clustered, exhibiting

Ecosystem-level studies of terrestrial carbon reveal contrasting bacterial metabolism in different aquatic habitats.

PubMed

Attermeyer, Katrin; Premke, Katrin; Hornick, Thomas; Hilt, Sabine; Grossart, Hans-Peter

2013-12-01

In aquatic systems, terrestrial dissolved organic matter (t-DOM) is known to stimulate bacterial activities in the water column, but simultaneous effects of autumnal leaf input on water column and sediment microbial dynamics in littoral zones of lakes remain largely unknown. The study's objective was to determine the effects of leaf litter on bacterial metabolism in the littoral water and sediment, and subsequently, the consequences for carbon cycling and food web dynamics. Therefore, in late fall, we simultaneously measured water and sediment bacterial metabolism in the littoral zone of a temperate shallow lake after adding terrestrial particulate organic matter (t-POM), namely, maize leaves. To better evaluate bacterial production (BP) and community respiration (CR) in sediments, we incubated sediment cores with maize leaves of different quality (nonleached and leached) under controlled laboratory conditions. Additionally, to quantify the incorporated leaf carbon into microbial biomass, we determined carbon isotopic ratios of fatty acids from sediment and leaf-associated microbes from a laboratory experiment using 13C-enriched beech leaves. The concentrations of dissolved organic carbon (DOC) increased significantly in the lake after the addition of maize leaves, accompanied by a significant increase in water BP. In contrast, sediment BP declined after an initial peak, showing no positive response to t-POM addition. Sediment BP and CR were also not stimulated by t-POM in the laboratory experiment, either in short-term or in long-term incubations, except for a short increase in CR after 18 hours. However, this increase might have reflected the metabolism of leaf-associated microorganisms. We conclude that the leached t-DOM is actively incorporated into microbial biomass in the water column but that the settling leached t-POM (t-POML) does not enter the food web via sediment bacteria. Consequently, t-POML is either buried in the sediment or introduced into the

Anion-Receptor Mediated Oxidation of Carbon Monoxide to Carbonate by Peroxide Dianion

DOE PAGES

Nava, Matthew; Lopez, Nazario; Muller, Peter; ...

2015-10-14

The reactivity of peroxide dianion O 2 2– has been scarcely explored in organic media due to the lack of soluble sources of this reduced oxygen species. We now report the finding that the encapsulated peroxide cryptate, [O 2cmBDCA-5t-H 6] 2– (1), reacts with carbon monoxide in organic solvents at 40 °C to cleanly form an encapsulated carbonate. Characterization of the resulting hexacarboxamide carbonate cryptate by single crystal X-ray diffraction reveals that carbonate dianion forms nine complementary hydrogen bonds with the hexacarboxamide cryptand, [CO 3cmBDCA-5t-H 6] 2– (2), a conclusion that is supported by spectroscopic data. Labeling studies and 17Omore » solid-state NMR data confirm that two-thirds of the oxygen atoms in the encapsulated carbonate derive from peroxide dianion, while the carbon is derived from CO. Further evidence for the formation of a carbonate cryptate was obtained by three methods of independent synthesis: treatment of (i) free cryptand with K 2CO 3; (ii) monodeprotonated cryptand with PPN[HCO 3]; and (iii) free cryptand with TBA[OH] and atmospheric CO 2. This work demonstrates CO oxidation mediated by a hydrogen-bonding anion receptor, constituting an alternative to transition-metal catalysis.« less

Total Organic Carbon Distribution and Bacterial Cycling Across A Geostrophic Front In Mediterranean Sea. Implications For The Western Basin Carbon Cycle

NASA Astrophysics Data System (ADS)

Sempere, R.; van Wambeke, F.; Bianchi, M.; Dafner, E.; Lefevre, D.; Bruyant, F.; Prieur, L.

We investigated the dynamic of the total organic carbon (TOC) pool and the role it played in the carbon cycle during winter 1997-1998 in the Almeria-Oran jet-front (AOF) system resulting from the spreading of Atlantic surface water through the Gibraltar Strait in the Alboran Sea (Southwestern Mediterranean Sea). We determined TOC by using high temperature combustion technique (HTC) and bacterial produc- tion (BP; via [3H] leucine incorporation) during two legs in the frontal area. We also estimated labile TOC (l-TOC) and bacterial growth efficiency (BGE) by performing TOC biodegradation experiments on board during the cruise whereas water column semi-labile (sl-TOC), and refractory-TOC were determined from TOC profile exami- nation. These results are discussed in relation with current velocity measured by using accoustic doppler current profiler (ADCP). Lowest TOC stocks (6330-6853 mmol C m-2) over 0-100 m were measured in the northern side of the geostrophic Jet which is also the highest dynamic area (horizontal speed of 80 cm s-1 in the first 100 m di- rected eastward). Our results indicated variable turnover times of sl-TOC across the Jet-Front system, which might be explained by different coupling of primary produc- tion and bacterial production observed in these areas. We also estimated TOC and sl-TOC transports within the Jet core off the Alboran Sea as well as potential CO2 production through bacterial respiration produced from sl-TOC assimilation by het- erotrophic bacteria.

Interaction of Uranium with Bacterial Cell Surfaces: Inferences from Phosphatase-Mediated Uranium Precipitation.

PubMed

Kulkarni, Sayali; Misra, Chitra Seetharam; Gupta, Alka; Ballal, Anand; Apte, Shree Kumar

2016-08-15

Deinococcus radiodurans and Escherichia coli expressing either PhoN, a periplasmic acid phosphatase, or PhoK, an extracellular alkaline phosphatase, were evaluated for uranium (U) bioprecipitation under two specific geochemical conditions (GCs): (i) a carbonate-deficient condition at near-neutral pH (GC1), and (ii) a carbonate-abundant condition at alkaline pH (GC2). Transmission electron microscopy revealed that recombinant cells expressing PhoN/PhoK formed cell-associated uranyl phosphate precipitate under GC1, whereas the same cells displayed extracellular precipitation under GC2. These results implied that the cell-bound or extracellular location of the precipitate was governed by the uranyl species prevalent at that particular GC, rather than the location of phosphatase. MINTEQ modeling predicted the formation of predominantly positively charged uranium hydroxide ions under GC1 and negatively charged uranyl carbonate-hydroxide complexes under GC2. Both microbes adsorbed 6- to 10-fold more U under GC1 than under GC2, suggesting that higher biosorption of U to the bacterial cell surface under GC1 may lead to cell-associated U precipitation. In contrast, at alkaline pH and in the presence of excess carbonate under GC2, poor biosorption of negatively charged uranyl carbonate complexes on the cell surface might have resulted in extracellular precipitation. The toxicity of U observed under GC1 being higher than that under GC2 could also be attributed to the preferential adsorption of U on cell surfaces under GC1. This work provides a vivid description of the interaction of U complexes with bacterial cells. The findings have implications for the toxicity of various U species and for developing biological aqueous effluent waste treatment strategies. The present study provides illustrative insights into the interaction of uranium (U) complexes with recombinant bacterial cells overexpressing phosphatases. This work demonstrates the effects of aqueous speciation of U on

Interaction of Uranium with Bacterial Cell Surfaces: Inferences from Phosphatase-Mediated Uranium Precipitation

PubMed Central

Kulkarni, Sayali; Misra, Chitra Seetharam; Gupta, Alka; Ballal, Anand

2016-01-01

ABSTRACT Deinococcus radiodurans and Escherichia coli expressing either PhoN, a periplasmic acid phosphatase, or PhoK, an extracellular alkaline phosphatase, were evaluated for uranium (U) bioprecipitation under two specific geochemical conditions (GCs): (i) a carbonate-deficient condition at near-neutral pH (GC1), and (ii) a carbonate-abundant condition at alkaline pH (GC2). Transmission electron microscopy revealed that recombinant cells expressing PhoN/PhoK formed cell-associated uranyl phosphate precipitate under GC1, whereas the same cells displayed extracellular precipitation under GC2. These results implied that the cell-bound or extracellular location of the precipitate was governed by the uranyl species prevalent at that particular GC, rather than the location of phosphatase. MINTEQ modeling predicted the formation of predominantly positively charged uranium hydroxide ions under GC1 and negatively charged uranyl carbonate-hydroxide complexes under GC2. Both microbes adsorbed 6- to 10-fold more U under GC1 than under GC2, suggesting that higher biosorption of U to the bacterial cell surface under GC1 may lead to cell-associated U precipitation. In contrast, at alkaline pH and in the presence of excess carbonate under GC2, poor biosorption of negatively charged uranyl carbonate complexes on the cell surface might have resulted in extracellular precipitation. The toxicity of U observed under GC1 being higher than that under GC2 could also be attributed to the preferential adsorption of U on cell surfaces under GC1. This work provides a vivid description of the interaction of U complexes with bacterial cells. The findings have implications for the toxicity of various U species and for developing biological aqueous effluent waste treatment strategies. IMPORTANCE The present study provides illustrative insights into the interaction of uranium (U) complexes with recombinant bacterial cells overexpressing phosphatases. This work demonstrates the effects of aqueous

Gallium-mediated growth of multiwall carbon nanotubes

NASA Astrophysics Data System (ADS)

Pan, Zheng Wei; Dai, Sheng; Beach, David B.; Evans, Neal D.; Lowndes, Douglas H.

2003-03-01

Liquid gallium was used as a viable and effective solvent and template for high-yield growth of multiwall carbon nanotubes. The gallium-mediated nanotubes thus obtained differ morphologically from nanotubes obtained by using transition metals as catalysts. The nanotubes have a pin-like morphology, generally composed of an oval-shaped tip filled with liquid gallium and a tapered hollow body. The inner diameter of the tube is so large that the inner/outer diameter ratio is usually larger than 0.9. The tubes are naturally opened at both ends. These gallium-filled nanotubes may be used as a nanothermometer in the temperature range of 30 to 550 °C. This study opens an interesting route for carbon nanotube synthesis.

Bacterial diversity and active biomass in full-scale granular activated carbon filters operated at low water temperatures.

PubMed

Kaarela, Outi E; Härkki, Heli A; Palmroth, Marja R T; Tuhkanen, Tuula A

2015-01-01

Granular activated carbon (GAC) filtration enhances the removal of natural organic matter and micropollutants in drinking water treatment. Microbial communities in GAC filters contribute to the removal of the biodegradable part of organic matter, and thus help to control microbial regrowth in the distribution system. Our objectives were to investigate bacterial community dynamics, identify the major bacterial groups, and determine the concentration of active bacterial biomass in full-scale GAC filters treating cold (3.7-9.5°C), physicochemically pretreated, and ozonated lake water. Three sampling rounds were conducted to study six GAC filters of different operation times and flow modes in winter, spring, and summer. Total organic carbon results indicated that both the first-step and second-step filters contributed to the removal of organic matter. Length heterogeneity analysis of amplified 16S rRNA genes illustrated that bacterial communities were diverse and considerably stable over time. α-Proteobacteria, β-Proteobacteria, and Nitrospira dominated in all of the GAC filters, although the relative proportion of dominant phylogenetic groups in individual filters differed. The active bacterial biomass accumulation, measured as adenosine triphosphate, was limited due to low temperature, low flux of nutrients, and frequent backwashing. The concentration of active bacterial biomass was not affected by the moderate seasonal temperature variation. In summary, the results provided an insight into the biological component of GAC filtration in cold water temperatures and the operational parameters affecting it.

Bacterial bioluminescence onset and quenching: a dynamical model for a quorum sensing-mediated property

PubMed Central

Side, Domenico Delle; Nassisi, Vincenzo; Pennetta, Cecilia; Alifano, Pietro; Di Salvo, Marco; Talà, Adelfia; Chechkin, Aleksei; Seno, Flavio

2017-01-01

We present an effective dynamical model for the onset of bacterial bioluminescence, one of the most studied quorum sensing-mediated traits. Our model is built upon simple equations that describe the growth of the bacterial colony, the production and accumulation of autoinducer signal molecules, their sensing within bacterial cells, and the ensuing quorum activation mechanism that triggers bioluminescent emission. The model is directly tested to quantitatively reproduce the experimental distributions of photon emission times, previously measured for bacterial colonies of Vibrio jasicida, a luminescent bacterium belonging to the Harveyi clade, growing in a highly drying environment. A distinctive and novel feature of the proposed model is bioluminescence ‘quenching’ after a given time elapsed from activation. Using an advanced fitting procedure based on the simulated annealing algorithm, we are able to infer from the experimental observations the biochemical parameters used in the model. Such parameters are in good agreement with the literature data. As a further result, we find that, at least in our experimental conditions, light emission in bioluminescent bacteria appears to originate from a subtle balance between colony growth and quorum activation due to autoinducers diffusion, with the two phenomena occurring on the same time scale. This finding is consistent with a negative feedback mechanism previously reported for Vibrio harveyi. PMID:29308273

Bacterial bioluminescence onset and quenching: a dynamical model for a quorum sensing-mediated property.

PubMed

Side, Domenico Delle; Nassisi, Vincenzo; Pennetta, Cecilia; Alifano, Pietro; Di Salvo, Marco; Talà, Adelfia; Chechkin, Aleksei; Seno, Flavio; Trovato, Antonio

2017-12-01

We present an effective dynamical model for the onset of bacterial bioluminescence, one of the most studied quorum sensing-mediated traits. Our model is built upon simple equations that describe the growth of the bacterial colony, the production and accumulation of autoinducer signal molecules, their sensing within bacterial cells, and the ensuing quorum activation mechanism that triggers bioluminescent emission. The model is directly tested to quantitatively reproduce the experimental distributions of photon emission times, previously measured for bacterial colonies of Vibrio jasicida , a luminescent bacterium belonging to the Harveyi clade, growing in a highly drying environment. A distinctive and novel feature of the proposed model is bioluminescence 'quenching' after a given time elapsed from activation. Using an advanced fitting procedure based on the simulated annealing algorithm, we are able to infer from the experimental observations the biochemical parameters used in the model. Such parameters are in good agreement with the literature data. As a further result, we find that, at least in our experimental conditions, light emission in bioluminescent bacteria appears to originate from a subtle balance between colony growth and quorum activation due to autoinducers diffusion, with the two phenomena occurring on the same time scale. This finding is consistent with a negative feedback mechanism previously reported for Vibrio harveyi .

Carbonate-mediated Mars-van Krevelen mechanism for CO oxidation on cobalt-doped ceria catalysts: facet-dependence and coordination-dependence.

PubMed

Liu, Bing; Li, Wenping; Song, Weiyu; Liu, Jian

2018-06-13

Carbonate intermediates have been reported to play an active role in CO oxidation over ceria-based catalysts in recent experimental studies. However, the detailed CO oxidation mechanism involving carbonate intermediates over ceria-based catalysts remains obscure. In this work, we carried out systematic density functional theory calculations corrected by on-site Coulomb interactions (DFT+U) to investigate the complete CO oxidation mechanism involving carbonate intermediates over cobalt-doped CeO2 catalysts, aiming to unravel how the carbonate participates in CO oxidation and shed light on the underlying factors that control the carbonate-mediated reaction mechanism. A novel carbonate-mediated Mars-van Krevelen (M-vK) mechanism was proposed, in which the carbonate acts as an active intermediate rather than a spectator and can react with CO to form CO2. This carbonate-mediated M-vK mechanism is facet-dependent because it is predominant on the (110) surface whereas the conventional M-vK mechanism is more favorable on (111) and (100) surfaces. The origin of facet-dependence was discussed by analyzing the geometric and electronic structures. It is found that the negatively charged bent CO2- intermediate formed on the (110) surface plays a critical role in the carbonate-mediated M-vK mechanism, whereas the formation of a neutral linear CO2 intermediate on (111) and (100) surfaces hinders the carbonate-mediated M-vK mechanism. The surface oxygen vacancy hinders the formation of carbonate intermediates, indicating that the carbonate-mediated M-vK mechanism is also vacancy-dependent. The formation of carbonate intermediates on different metal (Ti, V, W, Mo and Re) doped CeO2(110) surfaces was studied and the results indicate that the coordination environment of the dopant species is a key factor that determines the carbonate-mediated M-vK mechanism. This study provides atomic-scale insights into the reaction mechanism involving carbonate intermediates and the structure

The influence of dissolved organic carbon on bacterial phosphorus uptake and bacteria-phytoplankton dynamics in two Minnesota lakes

USGS Publications Warehouse

Stets, E.G.; Cotner, J.B.

2008-01-01

The balance of production in any ecosystem is dependent on the flow of limiting nutrients into either the autotrophic or heterotrophic components of the food web. To understand one of the important controls on the flow of inorganic nutrients between phytoplankton and bacterioplankton in lakes, we manipulated dissolved organic carbon (DOC) in two lakes of different trophic status. We hypothesized that labile DOC additions would increase bacterial phosphorus (P) uptake and decrease the response of phytoplankton to nutrient additions. Supplemental nutrients and carbon (C), nitrogen (N, 1.6 ??mol NH4Cl L-1 d-1), P (0.1 ??mol KH 2PO4 L-1 d-1), and DOC (glucose, 15 ??mol C L-1 d-1) were added twice daily to 8-liter experimental units. We tested the effect of added DOC on chlorophyll concentration, bacterial production, biomass, and P uptake using size-fractionated 33P-PO4 uptake. In the oligotrophic lake, DOC additions stimulated bacterial production and increased bacterial biomass-specific P uptake. Bacteria consumed added DOC, and chlorophyll concentrations were significantly lower in carboys receiving DOC additions. In the eutrophic lake, DOC additions had less of a stimulatory effect on bacterial production and biomass-specific P uptake. DOC accumulated over the time period, and there was little evidence for a DOC-induced decrease in phytoplankton biomass. Bacterial growth approached the calculated ??max and yet did not accumulate biomass, indicating significant biomass losses, which may have constrained bacterial DOC consumption. Excess bacterial DOC consumption in oligotrophic lakes may result in greater bacterial P affinity and enhanced nutrient uptake by the heterotrophic compartment of the food web. On the other hand, constraints on bacterial biomass accumulation in eutrophic lakes, from either viral lysis or bacterial grazing, can allow labile DOC to accumulate, thereby negating the effect of excess DOC on the planktonic food web. ?? 2008, by the American

Mediation analysis to estimate direct and indirect milk losses associated with bacterial load in bovine subclinical mammary infections.

PubMed

Detilleux, J; Theron, L; Duprez, J-N; Reding, E; Moula, N; Detilleux, M; Bertozzi, C; Hanzen, C; Mainil, J

2016-08-01

Milk losses associated with mastitis can be attributed to either effects of pathogens per se (i.e. direct losses) or to effects of the immune response triggered by the presence of mammary pathogens (i.e. indirect losses). Test-day milk somatic cell counts (SCC) and number of bacterial colony forming units (CFU) found in milk samples are putative measures of the level of immune response and of the bacterial load, respectively. Mediation models, in which one independent variable affects a second variable which, in turn, affects a third one, are conceivable models to estimate direct and indirect losses. Here, we evaluated the feasibility of a mediation model in which test-day SCC and milk were regressed toward bacterial CFU measured at three selected sampling dates, 1 week apart. We applied this method on cows free of clinical signs and with records on up to 3 test-days before and after the date of the first bacteriological samples. Most bacteriological cultures were negative (52.38%), others contained either staphylococci (23.08%), streptococci (9.16%), mixed bacteria (8.79%) or were contaminated (6.59%). Only losses mediated by an increase in SCC were significantly different from null. In cows with three consecutive bacteriological positive results, we estimated a decreased milk yield of 0.28 kg per day for each unit increase in log2-transformed CFU that elicited one unit increase in log2-transformed SCC. In cows with one or two bacteriological positive results, indirect milk loss was not significantly different from null although test-day milk decreased by 0.74 kg per day for each unit increase of log2-transformed SCC. These results highlight the importance of milk losses that are mediated by an increase in SCC during mammary infection and the feasibility of decomposing total milk loss into its direct and indirect components.

The impact of dissolved organic carbon and bacterial respiration on pCO2 in experimental sea ice

NASA Astrophysics Data System (ADS)

Zhou, J.; Kotovitch, M.; Kaartokallio, H.; Moreau, S.; Tison, J.-L.; Kattner, G.; Dieckmann, G.; Thomas, D. N.; Delille, B.

2016-02-01

Previous observations have shown that the partial pressure of carbon dioxide (pCO2) in sea ice brines is generally higher in Arctic sea ice compared to those from the Antarctic sea ice, especially in winter and early spring. We hypothesized that these differences result from the higher dissolved organic carbon (DOC) content in Arctic seawater: Higher concentrations of DOC in seawater would be reflected in a greater DOC incorporation into sea ice, enhancing bacterial respiration, which in turn would increase the pCO2 in the ice. To verify this hypothesis, we performed an experiment using two series of mesocosms: one was filled with seawater (SW) and the other one with seawater with an addition of filtered humic-rich river water (SWR). The addition of river water increased the DOC concentration of the water from a median of 142 μmol Lwater-1 in SW to 249 μmol Lwater-1 in SWR. Sea ice was grown in these mesocosms under the same physical conditions over 19 days. Microalgae and protists were absent, and only bacterial activity has been detected. We measured the DOC concentration, bacterial respiration, total alkalinity and pCO2 in sea ice and the underlying seawater, and we calculated the changes in dissolved inorganic carbon (DIC) in both media. We found that bacterial respiration in ice was higher in SWR: median bacterial respiration was 25 nmol C Lice-1 h-1 compared to 10 nmol C Lice-1 h-1 in SW. pCO2 in ice was also higher in SWR with a median of 430 ppm compared to 356 ppm in SW. However, the differences in pCO2 were larger within the ice interiors than at the surfaces or the bottom layers of the ice, where exchanges at the air-ice and ice-water interfaces might have reduced the differences. In addition, we used a model to simulate the differences of pCO2 and DIC based on bacterial respiration. The model simulations support the experimental findings and further suggest that bacterial growth efficiency in the ice might approach 0.15 and 0.2. It is thus credible

Assessment of bacterial growth and total organic carbon removal on granular activated carbon contactors.

PubMed Central

Bancroft, K; Maloney, S W; McElhaney, J; Suffet, I H; Pipes, W O

1983-01-01

The overall growth rate of bacteria on granular activated carbon (GAC) contactors at the Philadelphia Torresdale Water Treatment Pilot Plant facility was found to decrease until steady state was reached. The growth rate was found to fluctuate between 6.94 X 10(-3) and 8.68 X 10(-4) doublings per h. The microbiological removal of total organic carbon (TOC) was calculated by considering the GAC contactors as semiclosed continuous culture systems and using growth yield factors determined in laboratory experiments. After ozonation, the average TOC entering the contactors was 1,488 micrograms/liter, and the average effluent TOC was 497 micrograms/liter. Microbiological TOC removal was found to average 240 micrograms/liter on GAC contactors, which was not significantly different from microbiological TOC (220 micrograms/liter) removal across a parallel sand contactor where no adsorption took place. Thus, GAC did not appear to enhance biological TOC removal. Bacterial growth and maintenance was responsible for approximately 24% of the TOC removal on GAC under the conditions of this study. PMID:6639023

Assessment of bacterial growth and total organic carbon removal on granular activated carbon contactors.

PubMed

Bancroft, K; Maloney, S W; McElhaney, J; Suffet, I H; Pipes, W O

1983-09-01

The overall growth rate of bacteria on granular activated carbon (GAC) contactors at the Philadelphia Torresdale Water Treatment Pilot Plant facility was found to decrease until steady state was reached. The growth rate was found to fluctuate between 6.94 X 10(-3) and 8.68 X 10(-4) doublings per h. The microbiological removal of total organic carbon (TOC) was calculated by considering the GAC contactors as semiclosed continuous culture systems and using growth yield factors determined in laboratory experiments. After ozonation, the average TOC entering the contactors was 1,488 micrograms/liter, and the average effluent TOC was 497 micrograms/liter. Microbiological TOC removal was found to average 240 micrograms/liter on GAC contactors, which was not significantly different from microbiological TOC (220 micrograms/liter) removal across a parallel sand contactor where no adsorption took place. Thus, GAC did not appear to enhance biological TOC removal. Bacterial growth and maintenance was responsible for approximately 24% of the TOC removal on GAC under the conditions of this study.

Vacancy Mediated Mechanism of Nitrogen Substitution in Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, Madhu; Sadanadan, Bindu; Rao, Apparao M.

2003-01-01

Nitrogen substitution reaction in a graphene sheet and carbon nanotubes of different diameter are investigated using the generalized tight-binding molecular dynamics method. The formation of a vacancy in curved graphene sheet or a carbon nanotube is found to cause a curvature dependent local reconstruction of the surface. Our simulations and analysis show that vacancy mediated N substitution (rather than N chemisorption) is favored on the surface of nanotubes with diameter larger than 8 nm. This predicted value of the critical minimum diameter for N incorporation is confirmed by experimental results presented.

Activated carbon decreases invasive plant growth by mediating plant–microbe interactions

PubMed Central

Nolan, Nicole E.; Kulmatiski, Andrew; Beard, Karen H.; Norton, Jeanette M.

2015-01-01

There is growing appreciation for the idea that plant–soil interactions (e.g. allelopathy and plant–microbe feedbacks) may explain the success of some non-native plants. Where this is the case, native plant restoration may require management tools that change plant–soil interactions. Activated carbon (AC) is one such potential tool. Previous research has shown the potential for high concentrations of AC to restore native plant growth to areas dominated by non-natives on a small scale (1 m × 1 m plots). Here we (i) test the efficacy of different AC concentrations at a larger scale (15 m × 15 m plots), (ii) measure microbial responses to AC treatment and (iii) use a greenhouse experiment to identify the primary mechanism, allelopathy versus microbial changes, through which AC impacts native and non-native plant growth. Three years after large-scale applications, AC treatments decreased non-native plant cover and increased the ratio of native to non-native species cover, particularly at concentrations >400 g m−2. Activated carbon similarly decreased non-native plant growth in the greenhouse. This effect, however, was only observed in live soils, suggesting that AC effects were microbially mediated and not caused by direct allelopathy. Bacterial community analysis of field soils indicated that AC increased the relative abundance of an unidentified bacterium and an Actinomycetales and decreased the relative abundance of a Flavobacterium, suggesting that these organisms may play a role in AC effects on plant growth. Results support the idea that manipulations of plant–microbe interactions may provide novel and effective ways of directing plant growth and community development (e.g. native plant restoration). PMID:25387751

Bacterial Standing Stock, Activity, and Carbon Production during Formation and Growth of Sea Ice in the Weddell Sea, Antarctica.

PubMed

Grossmann, S; Dieckmann, G S

1994-08-01

Bacterial response to formation and growth of sea ice was investigated during autumn in the northeastern Weddell Sea. Changes in standing stock, activity, and carbon production of bacteria were determined in successive stages of ice development. During initial ice formation, concentrations of bacterial cells, in the order of 1 x 10 to 3 x 10 liter, were not enhanced within the ice matrix. This suggests that physical enrichment of bacteria by ice crystals is not effective. Due to low concentrations of phytoplankton in the water column during freezing, incorporation of bacteria into newly formed ice via attachment to algal cells or aggregates was not recorded in this study. As soon as the ice had formed, the general metabolic activity of bacterial populations was strongly suppressed. Furthermore, the ratio of [H]leucine incorporation into proteins to [H]thymidine incorporation into DNA changed during ice growth. In thick pack ice, bacterial activity recovered and growth rates up to 0.6 day indicated actively dividing populations. However, biomass-specific utilization of organic compounds remained lower than in open water. Bacterial concentrations of up to 2.8 x 10 cells liter along with considerably enlarged cell volumes accumulated within thick pack ice, suggesting reduced mortality rates of bacteria within the small brine pores. In the course of ice development, bacterial carbon production increased from about 0.01 to 0.4 mug of C liter h. In thick ice, bacterial secondary production exceeded primary production of microalgae.

Quorum Quenching: Enzymatic Disruption of N-Acylhomoserine Lactone-Mediated Bacterial Communication in Burkholderia thailandensis

DTIC Science & Technology

2004-10-01

lactonases failed to enhance beta-hemolytic activity. The results of this study demonstrate that heterologous expression of Bacillus sp . AiiA lactonases in...results of this study demonstrate that heterologous expression of Bacillus sp . AiiA lactonases in B. thailandensis reduced AHL accumulation, affected both...hemo- lysis, and carbon utilization by the expression of Bacillus sp . AiiA lactonases in B. thailandensis. MATERIALS AND METHODS Bacterial strains and

MPLA inhibits release of cytotoxic mediators from human neutrophils while preserving efficient bacterial killing.

PubMed

Ruchaud-Sparagano, Marie-Hélène; Mills, Ross; Scott, Jonathan; Simpson, A John

2014-10-01

Monophosphoryl lipid A (MPLA) is a lipopolysaccharides (LPS) derivative associated with neutrophil-dependent anti-inflammatory outcomes in animal models of sepsis. Little is known about the effect of MPLA on neutrophil function. This study sought to test the hypothesis that MPLA would reduce release of cytotoxic mediators from neutrophils without impairing bacterial clearance. Neutrophils were isolated from whole blood of healthy volunteers. The effects of MPLA and LPS on autologous serum-opsonised Pseudomonas aeruginosa killing by neutrophils and phagocytosis of autologous serum-opsonised zymosan were examined. Neutrophil oxidative burst, chemotaxis, enzyme and cytokine release as well as Toll-like receptor 4 (TLR4) expression were assessed following exposure to LPS or MPLA. LPS, but not MPLA, induced significant release of superoxide and myeloperoxidase from neutrophils. However, MPLA did not impair neutrophil capacity to ingest microbial particles and kill P. aeruginosa efficiently. MPLA was directly chemotactic for neutrophils, involving TLR4, p38 mitogen-activated protein kinase and tyrosine and alkaline phosphatases. LPS, but not MPLA, impaired N-formyl-methionyl-leucyl phenylalanine-directed migration of neutrophils, increased surface expression of TLR4, increased interleukin-8 release and strongly activated the myeloid differentiation primary response 88 pathway. Phosphoinositide 3-kinase inhibition significantly augmented IL-8 release from MPLA-treated neutrophils. The addition of MPLA to LPS-preincubated neutrophils led to a significant reduction in LPS-mediated superoxide release and TLR4 surface expression. Collectively, these findings suggest that MPLA directs efficient chemotaxis and bacterial killing in human neutrophils without inducing extracellular release of cytotoxic mediators and suggest that MPLA warrants further attention as a potential therapeutic in human sepsis.

Response of Bacterial Metabolic Activity to Riverine Dissolved Organic Carbon and Exogenous Viruses in Estuarine and Coastal Waters: Implications for CO2 Emission

PubMed Central

Xu, Jie; Sun, Mingming; Shi, Zhen; Harrison, Paul J.; Liu, Hongbin

2014-01-01

A cross-transplant experiment between estuarine water and seawater was conducted to examine the response of bacterial metabolic activity to riverine dissolved organic carbon (DOC) input under virus-rich and virus-free conditions, as well as to exogenous viruses. Riverine DOC input increased bacterial production significantly, but not bacterial respiration (BR) because of its high lability. The bioavailable riverine DOC influenced bulk bacterial respiration in two contrasting ways; it enhanced the bulk BR by stimulating bacterial growth, but simultaneously reduced the cell-specific BR due to its high lability. As a result, there was little stimulation of the bulk BR by riverine DOC. This might be partly responsible for lower CO2 degassing fluxes in estuaries receiving high sewage-DOC that is highly labile. Viruses restricted microbial decomposition of riverine DOC dramatically by repressing the growth of metabolically active bacteria. Bacterial carbon demand in the presence of viruses only accounted for 7–12% of that in the absence of viruses. Consequently, a large fraction of riverine DOC was likely transported offshore to the shelf. In addition, marine bacteria and estuarine bacteria responded distinctly to exogenous viruses. Marine viruses were able to infect estuarine bacteria, but not as efficiently as estuarine viruses, while estuarine viruses infected marine bacteria as efficiently as marine viruses. We speculate that the rapid changes in the viral community due to freshwater input destroyed the existing bacteria-virus relationship, which would change the bacterial community composition and affect the bacterial metabolic activity and carbon cycling in this estuary. PMID:25036641

Response of bacterial metabolic activity to riverine dissolved organic carbon and exogenous viruses in estuarine and coastal waters: implications for CO2 emission.

PubMed

Xu, Jie; Sun, Mingming; Shi, Zhen; Harrison, Paul J; Liu, Hongbin

2014-01-01

A cross-transplant experiment between estuarine water and seawater was conducted to examine the response of bacterial metabolic activity to riverine dissolved organic carbon (DOC) input under virus-rich and virus-free conditions, as well as to exogenous viruses. Riverine DOC input increased bacterial production significantly, but not bacterial respiration (BR) because of its high lability. The bioavailable riverine DOC influenced bulk bacterial respiration in two contrasting ways; it enhanced the bulk BR by stimulating bacterial growth, but simultaneously reduced the cell-specific BR due to its high lability. As a result, there was little stimulation of the bulk BR by riverine DOC. This might be partly responsible for lower CO2 degassing fluxes in estuaries receiving high sewage-DOC that is highly labile. Viruses restricted microbial decomposition of riverine DOC dramatically by repressing the growth of metabolically active bacteria. Bacterial carbon demand in the presence of viruses only accounted for 7-12% of that in the absence of viruses. Consequently, a large fraction of riverine DOC was likely transported offshore to the shelf. In addition, marine bacteria and estuarine bacteria responded distinctly to exogenous viruses. Marine viruses were able to infect estuarine bacteria, but not as efficiently as estuarine viruses, while estuarine viruses infected marine bacteria as efficiently as marine viruses. We speculate that the rapid changes in the viral community due to freshwater input destroyed the existing bacteria-virus relationship, which would change the bacterial community composition and affect the bacterial metabolic activity and carbon cycling in this estuary.

Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem.

PubMed

Rodríguez-Caballero, G; Caravaca, F; Fernández-González, A J; Alguacil, M M; Fernández-López, M; Roldán, A

2017-04-15

The main goal of this study was to assess the effect of the inoculation of four autochthonous shrub species with the arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices on the rhizosphere bacterial community and to ascertain whether such an effect is dependent on the host plant species. Additionally, analysis of rhizosphere soil chemical and biochemical properties was performed to find relationships between them and the rhizosphere bacterial communities. Non-metric multidimensional scaling analysis and subsequent permutational multivariate analysis of variance revealed differences in bacterial community composition and structure between non-inoculated and inoculated rhizospheres. Moreover, an influence of the plant species was observed. Different bacterial groups were found to be indicator taxonomic groups of non-inoculated and inoculated rhizospheres, Gemmatimonadetes and Anaerolineaceae, respectively, being the most notable indicators. As shown by distance based redundancy analysis, the shifts in bacterial community composition and structure mediated by the inoculation with the AM fungus were mainly related to changes in plant nutrients and growth parameters, such as the shoot phosphorus content. Our findings suggest that the AM fungal inoculum was able to modify the rhizosphere bacterial community assemblage while improving the host plant performance. Copyright © 2017 Elsevier B.V. All rights reserved.

Eicosanoids mediate nodulation reactions to bacterial infections in adults of two 17-year periodical cicadas, Magicicada septendecim and M. cassini.

PubMed

Tunaz, H; Bedick, J C.; Miller, J S.; Hoback, W W.; Rana, R L.; Stanley, D W.

1999-10-01

Nodulation is the first and quantitatively most important cellular defense reaction to bacterial infections in insects. Treating adults of the 17-year periodical cicadas, Magicicada septendecim and M. cassini, with eicosanoid biosynthesis inhibitors immediately prior to intrahemocoelic injections of the bacterium, Serratia marcescens, sharply reduced the nodulation response to bacterial challenges. Separate treatments with specific inhibitors of phospholipase A(2), cyclooxygenase, and lipoxygenase reduced nodulation, supporting our view that nodule formation is a multi-step process in which individual steps are separately mediated by lipoxygenase and cyclooxygenase products. The inhibitory influence of dexamethasone was apparent by 2 h after injection, and nodulation was significantly reduced, relative to control insects, over the following 14 h. The dexamethasone effects were reversed by treating bacteria-challenged insects with the eicosanoid-precursor polyunsaturated fatty acid, arachidonic acid. Low levels of arachidonic acid were detected in fat body phospholipids. These findings in adults of an exopterygote insect species with an unusual life history pattern broaden our hypothesis that eicosanoids mediate cellular immune reactions to bacterial infections in most, if not all, insects.

Derivatization of single-walled carbon nanotubes with redox mediator for biocatalytic oxygen electrodes.

PubMed

Sadowska, K; Stolarczyk, K; Biernat, J F; Roberts, K P; Rogalski, J; Bilewicz, R

2010-11-01

Single-walled carbon nanotubes (SWCNTs) were covalently modified with a redox mediator derived from 2,2'-azino-bis-(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS), and implemented in the construction of electrodes for biocatalytic oxygen reduction. The procedure is based on: covalent bonding of mediator to nanotubes, placing the nanotubes directly on the carbon electrode surface and covering the nanostructured electrode with a Nafion film containing laccase as the biocatalyst. The modified electrode is stable and the problem of mediator (ABTS) leaking from the film is eliminated by binding it covalently to the nanotubes. Three different synthetic approaches were used to obtain ABTS-modified carbon nanotubes. Nanotubes were modified at ends/defect sites or on the nanotube sidewalls and characterized by Raman spectroscopy, TGA and electrochemistry. The accessibility of differently located ABTS units by the laccase active center and mediation of electron transfer were studied by cyclic voltammetry. The surface concentrations of ABTS groups electrically connected with the electrode were compared for each of the electrodes based on the charges of the voltammetric peaks recorded in the deaerated solution. The nanotube modification procedure giving the best parameters of the catalytic process was selected. Copyright © 2010 Elsevier B.V. All rights reserved.

Salt-enhanced chemical weathering of building materials and bacterial mineralization of calcium carbonate as a treatment

NASA Astrophysics Data System (ADS)

Schiro, M.; Ruiz-Agudo, E.; Jroundi, F.; Gonzalez-Muñoz, M. T.; Rodriguez-Navarro, C.

2012-04-01

Salt weathering is an important mechanism contributing to the degradation and loss of stone building materials. In addition to the physical weathering resulting from crystallization pressure, the presence of salts in solution greatly enhances the chemical weathering potential of pore waters. Flow through experiments quantify the dissolution rates of calcite and quartz grains (63-125 micrometer diameter) when subjected to 1.0 ionic strength solutions of MgSO4, MgCl, Na2SO4 or NaCl. Results indicate that the identity of the cation is the primary control over the dissolution rate of both calcite and quartz substrates, with salt-enhanced dissolution occurring most rapidly in Mg2+ bearing solutions. It has been observed that weathering rates of rocks in nature, as well as building stones, are slowed down by naturally occurring or artificially produced patinas. These tend to be bacterially produced, durable mineralized coatings that lend some degree of protection to the underlying stone surface [1]. Our research shows that bacterially produced carbonate coatings can be quite effective at reducing chemical weathering of stone by soluble salts. The calcite-producing-bacteria used in this study were isolated from stone monuments in Granada, Spain [2] and cultivated in an organic-rich culture medium on a variety of artificial and natural substrates (including limestone, marble, sandstone, quartz, calcite single crystals, glass cover-slips, and sintered porous glass). Scanning electron microscopy (FESEM) was used to image bacterial calcite growth and biofilm formation. In-situ atomic force microscopy (AFM) enabled calculation of dissolution rates of untreated and bacterially treated surfaces. 2D-XRD showed the mineralogy and crystallographic orientation of bacterial calcium carbonate. Results indicate that bacterially produced calcite crystals form a coherent, mechanically resistant surface layer in perfect crystallographic continuity with the calcite substrate (self

Testing association between soil bacterial diversity and soil carbon storage on the Loess Plateau.

PubMed

Yang, Yang; Dou, Yanxing; An, Shaoshan

2018-06-01

Bacteria are widely distributed and play an important role in soil carbon (C) cycling. The impact of soil bacterial diversity on soil C storage has been well established, yet little is known about the underlying mechanisms and the interactions among them. Here, we examined the association between soil bacterial diversity and soil C storage in relation to vegetation restoration on the Loess Plateau. The dominant phyla among land use types (artificial forest, Af; natural shrubland, Ns; artificial grassland, Ag; natural grassland, Ng; slope cropland, Sc) were Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria, which transited from Acidobacteria-dominant to Actinobacteria-dominant community due to vegetation restoration. Soil C storage and the Shannon diversity index of soil bacterial community (H Bacteria ) showed the order Ns > Ng > Af > Ag > Sc, whereas no significant difference was found in Good's coverage (p > .05). Further, a strong relationship was observed between the relative abundance of dominant bacterial groups and soil C storage (p < .05). Additionally, soil bacterial diversity was closely related to soil C storage based on the structural equation model (SEM) and generalized additive models (GAMs). Specifically, soil C storage had the largest deterministic effects, explaining >70% of the variation and suggesting a strong association between soil C storage and soil bacterial diversity. Overall, we propose that further studies are necessary with a focus on the soil bacterial groups with specific functions in relation to soil C storage on the Loess Plateau. Copyright © 2018 Elsevier B.V. All rights reserved.

Bacterial growth and the decomposition of particulate organic carbon collected in sediment traps

NASA Astrophysics Data System (ADS)

Ducklow, Hugh W.; Hill, Suzanne M.; Gardner, Wilford D.

We have studied bacterial abundance and production in samples from sediment traps deployed for 1 and 100 days in several areas of the shelf and slope regions of the Middle Atlantic Bight, U.S.A. By making a series of assumptions about bacterial growth at the expense of POC in traps, we have estimated that the turnover time of organic particles collected in traps during long deployments is slow (mean 1500 ± 300 days), if only bacterial activity is considered. However the abundance and biomass of bacteria in traps is very high, ranging from 3 to 30 × 10 11 cells gC -1, i.e., 0.3 to 3% of the POC is bacterial carbon. Fifteen to 88% of the particles in traps were colonized by bacteria, but usually about half the particles had only 0 to 1 cell attached. Growth of bacteria was observed at all scales relevant to these trap deployments; over periods ranging from hours to weeks, at rates of 0.01 to 0.3 d -1. In spite of slow growth, bacteria appeared to be physiologically active in that [ 3H]adenine and [ 3H]thymidine were incorporated more rapidly into RNA and protein than into DNA. Total incorporation rates were high. We conclude that even relatively old (ca. 1 y) POC in sediment traps supports high levels of active bacterial biomass, but that POC decomposition is slow, so that bacteria may not be the principal agents of POC turnover following collection.

HLH-30/TFEB-mediated autophagy functions in a cell-autonomous manner for epithelium intrinsic cellular defense against bacterial pore-forming toxin in C. elegans.

PubMed

Chen, Huan-Da; Kao, Cheng-Yuan; Liu, Bang-Yu; Huang, Shin-Whei; Kuo, Cheng-Ju; Ruan, Jhen-Wei; Lin, Yen-Hung; Huang, Cheng-Rung; Chen, Yu-Hung; Wang, Horng-Dar; Aroian, Raffi V; Chen, Chang-Shi

2017-02-01

Autophagy is an evolutionarily conserved intracellular system that maintains cellular homeostasis by degrading and recycling damaged cellular components. The transcription factor HLH-30/TFEB-mediated autophagy has been reported to regulate tolerance to bacterial infection, but less is known about the bona fide bacterial effector that activates HLH-30 and autophagy. Here, we reveal that bacterial membrane pore-forming toxin (PFT) induces autophagy in an HLH-30-dependent manner in Caenorhabditis elegans. Moreover, autophagy controls the susceptibility of animals to PFT toxicity through xenophagic degradation of PFT and repair of membrane-pore cell-autonomously in the PFT-targeted intestinal cells in C. elegans. These results demonstrate that autophagic pathways and autophagy are induced partly at the transcriptional level through HLH-30 activation and are required to protect metazoan upon PFT intoxication. Together, our data show a new and powerful connection between HLH-30-mediated autophagy and epithelium intrinsic cellular defense against the single most common mode of bacterial attack in vivo.

In vitro bacterial cytotoxicity of CNTs: reactive oxygen species mediate cell damage edges over direct physical puncturing.

PubMed

Rajavel, Krishnamoorthy; Gomathi, Rajkumar; Manian, Sellamuthu; Rajendra Kumar, Ramasamy Thangavelu

2014-01-21

Understanding the bacterial cytotoxicity of CNTs is important for a wide variety of applications in the biomedical, environmental, and health sectors. A majority of the earlier reports attributed the bactericidal cytotoxicity of CNTs to bacterial cell membrane damage by direct physical puncturing. Our results reveal that bacterial cell death via bacterial cell membrane damage is induced by reactive oxygen species (ROS) produced from CNTs and is not due to direct physical puncturing by CNTs. To understand the actual mechanism of bacterial killing, we elucidated the bacterial cytotoxicity of SWCNTs and MWCNTs against Gram-negative human pathogenic bacterial species Escherichia coli, Shigella sonnei, Klebsiella pneumoniae, and Pseudomonas aeruginosa and its amelioration upon functionalizing the CNTs with antioxidant tannic acid (TA). Interestingly, the bacterial cells treated with CNTs exhibited severe cell damage under laboratory (ambient) and sunlight irradiation conditions. However, CNTs showed no cytotoxicity to the bacterial cells when incubated in the dark. The quantitative assessments carried out by us made it explicit that CNTs are effective generators of ROS such as (1)O2, O2(•-), and (•)OH in an aqueous medium under both ambient and sunlight-irradiated conditions. Both naked and TA-functionalized CNTs showed negligible ROS production in the dark. Furthermore, strong correlations were obtained between ROS produced by CNTs and the bacterial cell mortality (with the correlation coefficient varying between 0.7618 and 0.9891) for all four tested pathogens. The absence of bactericidal cytotoxicity in both naked and functionalized CNTs in the dark reveals that the presence of ROS is the major factor responsible for the bactericidal action compared to direct physical puncturing. This understanding of the bactericidal activity of the irradiated CNTs, mediated through the generation of ROS, could be interesting for novel applications such as regulated ROS delivery

Bartonella henselae engages inside-out and outside-in signaling by integrin β1 and talin1 during invasome-mediated bacterial uptake.

PubMed

Truttmann, Matthias C; Misselwitz, Benjamin; Huser, Sonja; Hardt, Wolf-Dietrich; Critchley, David R; Dehio, Christoph

2011-11-01

The VirB/D4 type IV secretion system (T4SS) of the bacterial pathogen Bartonella henselae (Bhe) translocates seven effector proteins (BepA-BepG) into human cells that subvert host cellular functions. Two redundant pathways dependent on BepG or the combination of BepC and BepF trigger the formation of a bacterial uptake structure termed the invasome. Invasome formation is a multi-step process consisting of bacterial adherence, effector translocation, aggregation of bacteria on the cell surface and engulfment, and eventually, complete internalization of the bacterial aggregate occurs in an F-actin-dependent manner. In the present study, we show that Bhe-triggered invasome formation depends on integrin-β1-mediated signaling cascades that enable assembly of the F-actin invasome structure. We demonstrate that Bhe interacts with integrin β1 in a fibronectin- and VirB/D4 T4SS-independent manner and that activated integrin β1 is essential for both effector translocation and the actin rearrangements leading to invasome formation. Furthermore, we show that talin1, but not talin2, is required for inside-out activation of integrin β1 during invasome formation. Finally, integrin-β1-mediated outside-in signaling by FAK, Src, paxillin and vinculin is necessary for invasome formation. This is the first example of a bacterial entry process that fully exploits the bi-directional signaling capacity of integrin receptors in a talin1-specific manner.

Enhanced photocatalytic activity of graphitic carbon nitride/carbon nanotube/Bi2WO6 ternary Z-scheme heterojunction with carbon nanotube as efficient electron mediator.

PubMed

Jiang, Deli; Ma, Wanxia; Xiao, Peng; Shao, Leqiang; Li, Di; Chen, Min

2018-02-15

All-solid-state Z-scheme heterojunction has attracted much attention in photocatalytic field because of its strong ability in charge separation and transfer. In the present study, all-solid-state ternary Z-scheme heterojunction constructed by graphitic carbon nitride (CN) nanosheet, carbon nanotube (CNT), and Bi 2 WO 6 (BWO) nanosheet, in which CNT was employed as the electron mediator. The CN/CNT/BWO ternary Z-scheme heterojunction shows the enhanced photocatalytic activity towards the degradation of tetracycline hydrochloride (TC) as compared to the pristine g-C 3 N 4 , Bi 2 WO 6 , CNT/BWO, CNT/CN, and CN/BWO. The significantly improved photocatalytic activity can be mainly ascribed to the formed CNT-mediated Z-scheme heterojunction, which facilitates the separation and transfer of photogenerated electron-hole pairs. Our work provides a rational design of all-solid-state Z-scheme heterojunction with CNT as the electron mediator for highly efficient photocatalysis. Copyright © 2017 Elsevier Inc. All rights reserved.

Hyperglycemia Impairs Neutrophil-Mediated Bacterial Clearance in Mice Infected with the Lyme Disease Pathogen.

PubMed

Javid, Ashkan; Zlotnikov, Nataliya; Pětrošová, Helena; Tang, Tian Tian; Zhang, Yang; Bansal, Anil K; Ebady, Rhodaba; Parikh, Maitry; Ahmed, Mijhgan; Sun, Chunxiang; Newbigging, Susan; Kim, Yae Ram; Santana Sosa, Marianna; Glogauer, Michael; Moriarty, Tara J

2016-01-01

Insulin-insufficient type 1 diabetes is associated with attenuated bactericidal function of neutrophils, which are key mediators of innate immune responses to microbes as well as pathological inflammatory processes. Neutrophils are central to immune responses to the Lyme pathogen Borrelia burgdorferi. The effect of hyperglycemia on host susceptibility to and outcomes of B. burgdorferi infection has not been examined. The present study investigated the impact of sustained obesity-independent hyperglycemia in mice on bacterial clearance, inflammatory pathology and neutrophil responses to B. burgdorferi. Hyperglycemia was associated with reduced arthritis incidence but more widespread tissue colonization and reduced clearance of bacterial DNA in multiple tissues including brain, heart, liver, lung and knee joint. B. burgdorferi uptake and killing were impaired in neutrophils isolated from hyperglycemic mice. Thus, attenuated neutrophil function in insulin-insufficient hyperglycemia was associated with reduced B. burgdorferi clearance in target organs. These data suggest that investigating the effects of comorbid conditions such as diabetes on outcomes of B. burgdorferi infections in humans may be warranted.

A uniform bacterial growth potential assay for different water types.

PubMed

Farhat, Nadia; Hammes, Frederik; Prest, Emmanuelle; Vrouwenvelder, Johannes

2018-06-06

The bacterial growth potential is important to understand and manage bacterial regrowth-related water quality concerns. Bacterial growth potential depends on growth promoting/limiting compounds, therefore, nutrient availability is the key factor governing bacterial growth potential. Selecting proper tools for bacterial growth measurement is essential for routine implementation of the growth potential measurement. This study proposes a growth potential assay that is universal and can be used for different water types and soil extract without restrictions of pure culture or cultivability of the bacterial strain. The proposed assay measures the sample bacterial growth potential by using the indigenous community as inocula. Flow cytometry (FCM) and adenosine tri-phosphate (ATP) were used to evaluate the growth potential of six different microbial communities indigenous to the sample being analyzed, with increasing carbon concentrations. Bottled mineral water, non-chlorinated tap water, seawater, river water, wastewater effluent and a soil organic carbon extract were analyzed. Results showed that indigenous bacterial communities followed normal batch growth kinetics when grown on naturally present organic carbon. Indigenous bacterial growth could detect spiked organic carbon concentrations as low as 10 μg/L. The indigenous community in all samples responded proportionally to the increase in acetate-carbon and proportional growth could be measured with both FCM and ATP. Bacterial growth was proportional to the carbon concentration but not the same proportion factor for the different water samples tested. The effect of inoculating the same water with different indigenous microbial communities on the growth potential was also examined. The FCM results showed that the highest increase in total bacterial cell concentration was obtained with bacteria indigenous to the water sample. The growth potential assay using indigenous bacterial community revealed consistent results

Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain.

PubMed

Kumar, Arvind; Rai, Lal Chand

2017-07-01

Soil quality is an important factor and maintained by inhabited microorganisms. Soil physicochemical characteristics determine indigenous microbial population and rice provides food security to major population of the world. Therefore, this study aimed to assess the impact of physicochemical variables on bacterial community composition and diversity in conventional paddy fields which could reflect a real picture of the bacterial communities operating in the paddy agro-ecosystem. To fulfill the objective; soil physicochemical characterization, bacterial community composition and diversity analysis was carried out using culture-independent PCR-DGGE method from twenty soils distributed across eight districts. Bacterial communities were grouped into three clusters based on UPGMA cluster analysis of DGGE banding pattern. The linkage of measured physicochemical variables with bacterial community composition was analyzed by canonical correspondence analysis (CCA). CCA ordination biplot results were similar to UPGMA cluster analysis. High levels of species-environment correlations (0.989 and 0.959) were observed and the largest proportion of species data variability was explained by total organic carbon (TOC), available nitrogen, total nitrogen and pH. Thus, results suggest that TOC and nitrogen are key regulators of bacterial community composition in the conventional paddy fields. Further, high diversity indices and evenness values demonstrated heterogeneity and co-abundance of the bacterial communities.

Effects of carbon dioxide on metabolite production and bacterial communities during kimchi fermentation.

PubMed

Park, Doo Hyun

2018-04-24

Bacterial communities and metabolites in kimchi fermented under conventional conditions (CC) compared to CO 2 -rich environments (CO 2 ) were analyzed. After a 20-day fermentation, lactic and acetic acid productions were 54 and 69 mM under CC, and 19 and 12 mM under CO 2 , respectively. The final pH of kimchi fermented under CC (CC-fermenting) and CO 2 (CO 2 -fermenting) were 4.1 and 4.7, respectively. For bacterial communities, OTU and Chao1 indices were both 35 in fresh kimchi, 10 and 15 in CC-fermenting kimchi, and 8 and 24 in CO 2 -fermenting kimchi, respectively. Shannon and Simpson indices were 3.47 and 0.93 in fresh kimchi, 1.87-0.06 and 0.46-0.01 in CC-fermenting kimchi, and 1.65-0.44 and 0.63-0.12 in CO 2 -fermenting kimchi, respectively. Non-lactic acid bacteria were eliminated in fermenting kimchi after 12 days under CC and 6 days under CO 2 . I conclude that carbon dioxide can alter bacterial communities, reduce metabolite production, and improve fermented kimchi quality.

Soil bacterial communities are shaped by temporal and environmental filtering: evidence from a long-term chronosequence.

PubMed

Freedman, Zachary; Zak, Donald R

2015-09-01

Soil microbial communities are abundant, hyper-diverse and mediate global biogeochemical cycles, but we do not yet understand the processes mediating their assembly. Current hypothetical frameworks suggest temporal (e.g. dispersal limitation) and environmental (e.g. soil pH) filters shape microbial community composition; however, there is limited empirical evidence supporting this framework in the hyper-diverse soil environment, particularly at large spatial (i.e. regional to continental) and temporal (i.e. 100 to 1000 years) scales. Here, we present evidence from a long-term chronosequence (4000 years) that temporal and environmental filters do indeed shape soil bacterial community composition. Furthermore, nearly 20 years of environmental monitoring allowed us to control for potentially confounding environmental variation. Soil bacterial communities were phylogenetically distinct across the chronosequence. We determined that temporal and environmental factors accounted for significant portions of bacterial phylogenetic structure using distance-based linear models. Environmental factors together accounted for the majority of phylogenetic structure, namely, soil temperature (19%), pH (17%) and litter carbon:nitrogen (C:N; 17%). However, of all individual factors, time since deglaciation accounted for the greatest proportion of bacterial phylogenetic structure (20%). Taken together, our results provide empirical evidence that temporal and environmental filters act together to structure soil bacterial communities across large spatial and long-term temporal scales. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparative metabolomic analysis highlights the involvement of sugars and glycerol in melatonin-mediated innate immunity against bacterial pathogen in Arabidopsis

PubMed Central

Qian, Yongqiang; Tan, Dun-Xian; Reiter, Russel J.; Shi, Haitao

2015-01-01

Melatonin is an important secondary messenger in plant innate immunity against the bacterial pathogen Pseudomonas syringe pv. tomato (Pst) DC3000 in the salicylic acid (SA)- and nitric oxide (NO)-dependent pathway. However, the metabolic homeostasis in melatonin-mediated innate immunity is unknown. In this study, comparative metabolomic analysis found that the endogenous levels of both soluble sugars (fructose, glucose, melibose, sucrose, maltose, galatose, tagatofuranose and turanose) and glycerol were commonly increased after both melatonin treatment and Pst DC3000 infection in Arabidopsis. Further studies showed that exogenous pre-treatment with fructose, glucose, sucrose, or glycerol increased innate immunity against Pst DC3000 infection in wild type (Col-0) Arabidopsis plants, but largely alleviated their effects on the innate immunity in SA-deficient NahG plants and NO-deficient mutants. This indicated that SA and NO are also essential for sugars and glycerol-mediated disease resistance. Moreover, exogenous fructose, glucose, sucrose and glycerol pre-treatments remarkably increased endogenous NO level, but had no significant effect on the endogenous melatonin level. Taken together, this study highlights the involvement of sugars and glycerol in melatonin-mediated innate immunity against bacterial pathogen in SA and NO-dependent pathway in Arabidopsis. PMID:26508076

Carbon dioxide released from subduction zones by fluid-mediated reactions

NASA Astrophysics Data System (ADS)

Ague, Jay J.; Nicolescu, Stefan

2014-05-01

The balance between the subduction of carbonate mineral-bearing rocks into Earth's mantle and the return of CO2 to the atmosphere by volcanic and metamorphic degassing is critical to the carbon cycle. Carbon is thought to be released from subducted rocks mostly by simple devolatilization reactions. However, these reactions will also retain large amounts of carbon within the subducting slab and have difficulty in accounting for the mass of CO2 emitted from volcanic arcs. Carbon release may therefore occur via fluid-induced dissolution of calcium carbonate. Here we use carbonate δ18O and δ13C systematics, combined with analyses of rock and fluid inclusion mineralogy and geochemistry, to investigate the alteration of the exhumed Eocene Cycladic subduction complex on the Syros and Tinos islands, Greece. We find that in marble rocks adjacent to two fluid conduits that were active during subduction, the abundance of calcium carbonate drastically decreases approaching the conduits, whereas silicate minerals increase. Up to 60-90% of the CO2 was released from the rocks--far greater than expected via simple devolatilization reactions. The δ18O of the carbonate minerals is 5-10 lighter than is typical for metamorphosed carbonate rocks, implying that isotopically light oxygen was transported by fluid infiltration from the surroundings. We suggest that fluid-mediated carbonate mineral removal, accompanied by silicate mineral precipitation, provides a mechanism for the release of enormous amounts of CO2 from subduction zones.

The role microbial sulfate reduction in the direct mediation of sedimentary authigenic carbonate precipitation

NASA Astrophysics Data System (ADS)

Turchyn, A. V.; Walker, K.; Sun, X.

2016-12-01

The majority of modern deep marine sediments are bathed in water that is undersaturated with respect to calcium carbonate. However, within marine sediments changing chemical conditions, driven largely by the microbial oxidation of organic carbon in the absence of oxygen, lead to supersaturated conditions and drive calcium carbonate precipitation. This sedimentary calcium carbonate is often called `authigenic carbonate', and is found in the form of cements and disseminated crystals within the marine sedimentary pile. As this precipitation of this calcium carbonate is microbially mediated, identifying authigenic carbonate within the geological record and understanding what information its geochemical and/or isotopic signature may hold is key for understanding its importance and what information it may contain past life. However, the modern controls on authigenic carbonate precipitation remain enigmatic because the myriad of microbially mediated reactions occurring within sediments both directly and indirectly impact the proton balance. In this submission we present data from 25 ocean sediment cores spanning the globe where we explore the deviation from the stoichiometrically predicted relationships among alkalinity, calcium and sulfate concentrations. In theory for every mol of organic carbon reduced by sulfate, two mol of alkalinity is produced, and to precipitate subsurface calcium carbonate one mol of calcium is used to consume two mol of alkalinity. We use this data with a model to explore changes in carbonate saturation state with depth below the seafloor. Alkalinity changes in the subsurface are poorly correlated with changes in calcium concentrations, however calcium concentrations are directly and tightly coupled to changes in sulfate concentrations in all studied sites. This suggests a direct role for sulfate reducing bacteria in the precipitation of subsurface carbonate cements.

Seasonal variation in the biocontrol efficiency of bacterial wilt is driven by temperature-mediated changes in bacterial competitive interactions.

PubMed

Wei, Zhong; Huang, Jianfeng; Yang, Tianjie; Jousset, Alexandre; Xu, Yangchun; Shen, Qirong; Friman, Ville-Petri

2017-10-01

Microbe-based biocontrol applications hold the potential to become an efficient way to control plant pathogen disease outbreaks in the future. However, their efficiency is still very variable, which could be due to their sensitivity to the abiotic environmental conditions.Here, we assessed how environmental temperature variation correlates with ability of Ralstonia pickettii , an endophytic bacterial biocontrol agent, to suppress the Ralstonia solanacearum pathogen during different tomato crop seasons in China.We found that suppression of the pathogen was highest when the seasonal mean temperatures were around 20 °C and rapidly decreased with increasing mean crop season temperatures. Interestingly, low levels of disease incidence did not correlate with low pathogen or high biocontrol agent absolute densities. Instead, the biocontrol to pathogen density ratio was a more important predictor of disease incidence levels between different crop seasons. To understand this mechanistically, we measured the growth and strength of competition between the biocontrol agent and the pathogen over a naturally occurring temperature gradient in vitro . We found that the biocontrol strain grew relatively faster at low temperature ranges, and the pathogen at high temperature ranges, and that similar to field experiments, pathogen suppression peaked at 20 °C.Together, our results suggest that temperature-mediated changes in the strength of bacterial competition could potentially explain the variable R. solanacearum biocontrol outcomes between different crop seasons in China. Synthesis and applications . Our results suggest that abiotic environmental conditions, such as temperature, can affect the efficacy of biocontrol applications. Thus, in order to develop more consistent biocontrol applications in the future, we might need to find and isolate bacterial strains that can retain their functionality regardless of the changing environmental conditions.

Microalgal bacterial floc properties are improved by a balanced inorganic/organic carbon ratio.

PubMed

Van Den Hende, Sofie; Vervaeren, Han; Saveyn, Hans; Maes, Guy; Boon, Nico

2011-03-01

Microalgal bacterial floc (MaB-floc) reactors have been suggested as a more sustainable secondary wastewater treatment. We investigated whether MaB-flocs could be used as tertiary treatment. Tertiary influent has a high inorganic/organic carbon ratio, depending on the efficiency of the secondary treatment. In this study, the effect of this inorganic/organic carbon ratio on the MaB-flocs performance was determined, using three sequencing batch photobioreactors. The MaB-flocs were fed with synthetic wastewater containing 84, 42, and 0 mg L(-1) C-KHCO(3) supplemented with 0, 42, 84 mg L(-1) C-sucrose, respectively, representing inorganic versus organic carbon. Bicarbonate significantly decreased the autotrophic index of the MaB-flocs and resulted in poorly settling flocs. Moreover, sole bicarbonate addition led to a high pH of 9.5 and significant lower nitrogen removal efficiencies. Sucrose without bicarbonate resulted in good settling MaB-flocs, high nitrogen removal efficiencies and neutral pH levels. Despite the lower chlorophyll a content of the biomass and the lower in situ oxygen concentration, 92-96% of the soluble COD-sucrose was removed. This study shows that the inorganic/organic carbon ratio of the wastewater is of major importance and that organic carbon is requisite to guarantee a good performance of the MaB-flocs for wastewater treatment. Copyright © 2010 Wiley Periodicals, Inc.

Production of long chain alkyl esters from carbon dioxide and electricity by a two-stage bacterial process.

PubMed

Lehtinen, Tapio; Efimova, Elena; Tremblay, Pier-Luc; Santala, Suvi; Zhang, Tian; Santala, Ville

2017-11-01

Microbial electrosynthesis (MES) is a promising technology for the reduction of carbon dioxide into value-added multicarbon molecules. In order to broaden the product profile of MES processes, we developed a two-stage process for microbial conversion of carbon dioxide and electricity into long chain alkyl esters. In the first stage, the carbon dioxide is reduced to organic compounds, mainly acetate, in a MES process by Sporomusa ovata. In the second stage, the liquid end-products of the MES process are converted to the final product by a second microorganism, Acinetobacter baylyi in an aerobic bioprocess. In this proof-of-principle study, we demonstrate for the first time the bacterial production of long alkyl esters (wax esters) from carbon dioxide and electricity as the sole sources of carbon and energy. The process holds potential for the efficient production of carbon-neutral chemicals or biofuels. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates

NASA Astrophysics Data System (ADS)

Pönisch, Wolfram; Weber, Christoph A.; Juckeland, Guido; Biais, Nicolas; Zaburdaev, Vasily

2017-01-01

Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.

Synergistic Processing of Biphenyl and Benzoate: Carbon Flow Through the Bacterial Community in Polychlorinated-Biphenyl-Contaminated Soil

NASA Astrophysics Data System (ADS)

Leewis, Mary-Cathrine; Uhlik, Ondrej; Leigh, Mary Beth

2016-02-01

Aerobic mineralization of PCBs, which are toxic and persistent organic pollutants, involves the upper (biphenyl, BP) and lower (benzoate, BZ) degradation pathways. The activity of different members of the soil microbial community in performing one or both pathways, and their synergistic interactions during PCB biodegradation, are not well understood. This study investigates BP and BZ biodegradation and subsequent carbon flow through the microbial community in PCB-contaminated soil. DNA stable isotope probing (SIP) was used to identify the bacterial guilds involved in utilizing 13C-biphenyl (unchlorinated analogue of PCBs) and/or 13C-benzoate (product/intermediate of BP degradation and analogue of chlorobenzoates). By performing SIP with two substrates in parallel, we reveal microbes performing the upper (BP) and/or lower (BZ) degradation pathways, and heterotrophic bacteria involved indirectly in processing carbon derived from these substrates (i.e. through crossfeeding). Substrate mineralization rates and shifts in relative abundance of labeled taxa suggest that BP and BZ biotransformations were performed by microorganisms with different growth strategies: BZ-associated bacteria were fast growing, potentially copiotrophic organisms, while microbes that transform BP were oligotrophic, slower growing, organisms. Our findings provide novel insight into the functional interactions of soil bacteria active in processing biphenyl and related aromatic compounds in soil, revealing how carbon flows through a bacterial community.

Bacterial Associates Modify Growth Dynamics of the Dinoflagellate Gymnodinium catenatum

PubMed Central

Bolch, Christopher J. S.; Bejoy, Thaila A.; Green, David H.

2017-01-01

Marine phytoplankton cells grow in close association with a complex microbial associate community known to affect the growth, behavior, and physiology of the algal host. The relative scale and importance these effects compared to other major factors governing algal cell growth remain unclear. Using algal-bacteria co-culture models based on the toxic dinoflagellate Gymnodinium catenatum, we tested the hypothesis that associate bacteria exert an independent effect on host algal cell growth. Batch co-cultures of G. catenatum were grown under identical environmental conditions with simplified bacterial communities composed of one-, two-, or three-bacterial associates. Modification of the associate community membership and complexity induced up to four-fold changes in dinoflagellate growth rate, equivalent to the effect of a 5°C change in temperature or an almost six-fold change in light intensity (20–115 moles photons PAR m-2 s-1). Almost three-fold changes in both stationary phase cell concentration and death rate were also observed. Co-culture with Roseobacter sp. DG874 reduced dinoflagellate exponential growth rate and led to a more rapid death rate compared with mixed associate community controls or co-culture with either Marinobacter sp. DG879, Alcanivorax sp. DG881. In contrast, associate bacteria concentration was positively correlated with dinoflagellate cell concentration during the exponential growth phase, indicating growth was limited by supply of dinoflagellate-derived carbon. Bacterial growth increased rapidly at the onset of declining and stationary phases due to either increasing availability of algal-derived carbon induced by nutrient stress and autolysis, or at mid-log phase in Roseobacter co-cultures potentially due to the onset of bacterial-mediated cell lysis. Co-cultures with the three bacterial associates resulted in dinoflagellate and bacterial growth dynamics very similar to more complex mixed bacterial community controls, suggesting that

Contribution of heterotrophic bacterial production to the carbon budget of the river Seine (France).

PubMed

Servais, P; Garnier, J

1993-01-01

Bacterial activity was measured in the river Seine by two methods, (3)H-thymidine incorporation into DNA and (3)H-leucine incorporation into proteins. Both incorporation rates are characterized by low values upstream of Paris, a large increase just downstream of the outfall of the Achères treatment plant effluents, and then decreasing values further downstream. The covariation of both activities is demonstrated by the constancy of the molar ratio (leucine to thymidine incorporation rate) in the range of 6 to 8 for all the samples, except in the perturbed area where it is higher (15 to 35). These high values of molar ratio are linked to the introduction into the river of large sized bacteria ([Symbol: see text]1 µm) with higher incorporation rates per cell or biomass unit than the small autochthonous bacteria (< 1 µm). Growth rates of large bacteria were on average 3.7 times higher than those of small bacteria. Bacterial production was calculated with experimentally determined conversion factors (0.5 × 10(18) cells per mole of thymidine incorporated and 900 gC per mole of leucine incorporated) and by taking into account the activity of both size classes of bacteria measured through fractionation experiments (post-incubation filtration). Production estimated in the perturbed area downstream of Ach6res was very high, up to 60 µgC liter(-1)h(-1) in the summer. Carbon consumption by bacteria in the area perturbed by the Ach6res effluents was calculated assuming a growth yield of 0.2 and compared to the load of biodegradable organic matter discharged by the treatment plant. In summer, an additional supply of organic matter is required to account for the intense bacterial activity, suggesting the importance of phytoplankton production in the carbon budget.

Significance of bacteria and viruses in the carbon flow of tropical freshwater impoundments

NASA Astrophysics Data System (ADS)

Peduzzi, P.; Schiemer, F.

2003-04-01

In two types of tropical freshwater impoundments, free and particle-attached bacterial abundance and production as well as virus abundance, frequency of viral infection and virus production were investigated together with a set of environmental factors during two characteristic seasons. Organic nitrogen, phosphorus species, dissolved organic carbon and suspended solids were elevated in the wind-mixed water body of a shallow reservoir during the dry season, whereas a deeper reservoir type exhibited no obvious seasonality in these parameters. In SYBR GREEN-stained samples, bacterial abundance showed no seasonal pattern in either reservoir type. A large proportion of the overall bacterial production was associated with particulate material. Highest densities of virus particles and elevated frequency of bacteria containing mature phages were observed in the shallow reservoir during the dry season. The specific bacterial production was related to the abundance of particulate organic matter, phosphorus species and organic nitrogen. Most virus parameters were positively linked to bacterial density, production and to organic nitrogen. We calculated that between 13.2 and 46.1% of the bacterial standing stocks would be subjected to virus-mediated mortality. Carbon budgets for the microbial and organic matter compartments of these tropical freshwater reservoirs indicate prevailing autotrophy and a substantial pathway through the viral shunt. During the dry season the shallow, wind-mixed reservoir provided favorable conditions for bacterial growth and virus propagation.

Organic carbon source and salinity shape sediment bacterial composition in two China marginal seas and their major tributaries.

PubMed

Wang, Kai; Zou, Li; Lu, Xinxin; Mou, Xiaozhen

2018-08-15

Marginal sea sediments receive organic substrates of different origins, but whether and to what extent sediment microbial communities are reflective of the different sources of organic substrates remain unclear. To address these questions, sediment samples were collected in two connected China marginal seas, i.e., Bohai Sea and Yellow Sea, and their two major tributaries (Yellow River and Liao River). Sediment bacterial community composition (BCC) was examined using 16S rRNA gene pyrosequencing. In addition, physicochemical variables that describe environmental conditions and sediment features were measured. Our results revealed that BCCs changed with salinity and organic carbon (OC) content. Members of Gaiellaceae and Comamonadaceae showed a rapid decrease as salinity and phytoplankton-derived OC increased, while Piscirickettsiaceae and Desulfobulbaceae exhibited an opposite distribution pattern. Differences of riverine vs. marginal sea sediment BCCs could be mostly explained by salinity. However, within the marginal seas, sediment BCC variations were mainly explained by OC-related variables, including terrestrial-derived fatty acids (Terr_FA), phytoplankton-derived polyunsaturated fatty acids (Phyto_PUFA), stable carbon isotopes (δ 13 C), and carbon to nitrogen ratio (C/N). In addition to environmental variables, network analysis suggested that interactions among individual bacterial taxa might be important in shaping sediment BCCs in the studied areas. Copyright © 2018 Elsevier B.V. All rights reserved.

Distinct Cellular Locations of Carbonic Anhydrases Mediate Carbon Dioxide Control of Stomatal Movements

DOE PAGES

Hu, Honghong; Rappel, Wouter-Jan; Occhipinti, Rossana; ...

2015-09-28

Elevated carbon dioxide (CO 2) in leaves closes stomatal apertures. Research has shown key functions of the β-carbonic anhydrases (βCA1 and βCA4) in rapid CO 2-induced stomatal movements by catalytic transmission of the CO 2 signal in guard cells. But, the underlying mechanisms remain unclear, because initial studies indicate that these Arabidopsis (Arabidopsis thaliana) βCAs are targeted to distinct intracellular compartments upon expression in tobacco (Nicotiana benthamiana) cells. Which cellular location of these enzymes plays a key role in native guard cells in CO 2-regulated stomatal movements remains unknown. We express fluorescently tagged CAs in guard cells of ca1ca4 double-mutantmore » plants and show that the specific locations of βCA4 at the plasma membrane and βCA1 in native guard cell chloroplasts each can mediate rapid CO 2 control of stomatal movements. Localization and complementation analyses using a mammalian αCAII-yellow fluorescent protein in guard cells further show that cytoplasmic localization is also sufficient to restore CO 2 regulation of stomatal conductance. Mathematical modeling of cellular CO 2 catalysis suggests that the dynamics of the intracellular HCO 3 - concentration change in guard cells can be driven by plasma membrane and cytoplasmic localizations of CAs but not as clearly by chloroplast targeting. Therefore, modeling supports the notion that the intracellular HCO 3 - concentration dynamics in guard cells are a key mechanism in mediating CO 2 -regulated stomatal movements but that an additional chloroplast role of CAs exists that has yet to be identified.« less

Etiologic Diagnosis of Lower Respiratory Tract Bacterial Infections Using Sputum Samples and Quantitative Loop-Mediated Isothermal Amplification

PubMed Central

Peng, Peichao; Cheng, Xiaoxing; Wang, Guoqing; Qian, Minping; Gao, Huafang; Han, Bei; Chen, Yusheng; Hu, Yinghui; Geng, Rong; Hu, Chengping; Zhang, Wei; Yang, Jingping; Wan, Huanying; Yu, Qin; Wei, Liping; Li, Jiashu; Tian, Guizhen; Wang, Qiuyue; Hu, Ke; Wang, Siqin; Wang, Ruiqin; Du, Juan; He, Bei; Ma, Jianjun; Zhong, Xiaoning; Mu, Lan; Cai, Shaoxi; Zhu, Xiangdong; Xing, Wanli; Yu, Jun; Deng, Minghua; Gao, Zhancheng

2012-01-01

Etiologic diagnoses of lower respiratory tract infections (LRTI) have been relying primarily on bacterial cultures that often fail to return useful results in time. Although DNA-based assays are more sensitive than bacterial cultures in detecting pathogens, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. Here we report a nationwide cohort study on 2986 suspected LRTI patients across P. R. China. We compared the performance of a DNA-based assay qLAMP (quantitative Loop-mediated isothermal AMPlification) with that of standard bacterial cultures in detecting a panel of eight common respiratory bacterial pathogens from sputum samples. Our qLAMP assay detects the panel of pathogens in 1047(69.28%) patients from 1533 qualified patients at the end. We found that the bacterial titer quantified based on qLAMP is a predictor of probability that the bacterium in the sample can be detected in culture assay. The relatedness of the two assays fits a logistic regression curve. We used a piecewise linear function to define breakpoints where latent pathogen abruptly change its competitive relationship with others in the panel. These breakpoints, where pathogens start to propagate abnormally, are used as cutoffs to eliminate the influence of contaminations from normal flora. With help of the cutoffs derived from statistical analysis, we are able to identify causative pathogens in 750 (48.92%) patients from qualified patients. In conclusion, qLAMP is a reliable method in quantifying bacterial titer. Despite the fact that there are always latent bacteria contaminated in sputum samples, we can identify causative pathogens based on cutoffs derived from statistical analysis of competitive relationship. Trial Registration ClinicalTrials.gov NCT00567827 PMID:22719933

RNA-Seq analysis reveals insight into enhanced rice Xa7-mediated bacterial blight resistance at high temperature.

PubMed

Cohen, Stephen P; Liu, Hongxia; Argueso, Cristiana T; Pereira, Andy; Vera Cruz, Casiana; Verdier, Valerie; Leach, Jan E

2017-01-01

Plant disease is a major challenge to agriculture worldwide, and it is exacerbated by abiotic environmental factors. During some plant-pathogen interactions, heat stress allows pathogens to overcome host resistance, a phenomenon which could severely impact crop productivity considering the global warming trends associated with climate change. Despite the importance of this phenomenon, little is known about the underlying molecular mechanisms. To better understand host plant responses during simultaneous heat and pathogen stress, we conducted a transcriptomics experiment for rice plants (cultivar IRBB61) containing Xa7, a bacterial blight disease resistance (R) gene, that were infected with Xanthomonas oryzae, the bacterial blight pathogen of rice, during high temperature stress. Xa7-mediated resistance is unusual relative to resistance mediated by other R genes in that it functions better at high temperatures. Using RNA-Seq technology, we identified 8,499 differentially expressed genes as temperature responsive in rice cultivar IRBB61 experiencing susceptible and resistant interactions across three time points. Notably, genes in the plant hormone abscisic acid biosynthesis and response pathways were up-regulated by high temperature in both mock-treated plants and plants experiencing a susceptible interaction and were suppressed by high temperature in plants exhibiting Xa7-mediated resistance. Genes responsive to salicylic acid, an important plant hormone for disease resistance, were down-regulated by high temperature during both the susceptible and resistant interactions, suggesting that enhanced Xa7-mediated resistance at high temperature is not dependent on salicylic acid signaling. A DNA sequence motif similar to known abscisic acid-responsive cis-regulatory elements was identified in the promoter region upstream of genes up-regulated in susceptible but down-regulated in resistant interactions. The results of our study suggest that the plant hormone abscisic

RNA-Seq analysis reveals insight into enhanced rice Xa7-mediated bacterial blight resistance at high temperature

PubMed Central

Argueso, Cristiana T.; Pereira, Andy; Vera Cruz, Casiana; Verdier, Valerie

2017-01-01

Plant disease is a major challenge to agriculture worldwide, and it is exacerbated by abiotic environmental factors. During some plant-pathogen interactions, heat stress allows pathogens to overcome host resistance, a phenomenon which could severely impact crop productivity considering the global warming trends associated with climate change. Despite the importance of this phenomenon, little is known about the underlying molecular mechanisms. To better understand host plant responses during simultaneous heat and pathogen stress, we conducted a transcriptomics experiment for rice plants (cultivar IRBB61) containing Xa7, a bacterial blight disease resistance (R) gene, that were infected with Xanthomonas oryzae, the bacterial blight pathogen of rice, during high temperature stress. Xa7-mediated resistance is unusual relative to resistance mediated by other R genes in that it functions better at high temperatures. Using RNA-Seq technology, we identified 8,499 differentially expressed genes as temperature responsive in rice cultivar IRBB61 experiencing susceptible and resistant interactions across three time points. Notably, genes in the plant hormone abscisic acid biosynthesis and response pathways were up-regulated by high temperature in both mock-treated plants and plants experiencing a susceptible interaction and were suppressed by high temperature in plants exhibiting Xa7-mediated resistance. Genes responsive to salicylic acid, an important plant hormone for disease resistance, were down-regulated by high temperature during both the susceptible and resistant interactions, suggesting that enhanced Xa7-mediated resistance at high temperature is not dependent on salicylic acid signaling. A DNA sequence motif similar to known abscisic acid-responsive cis-regulatory elements was identified in the promoter region upstream of genes up-regulated in susceptible but down-regulated in resistant interactions. The results of our study suggest that the plant hormone abscisic

Utilization of Glyphosate as Phosphate Source: Biochemistry and Genetics of Bacterial Carbon-Phosphorus Lyase

PubMed Central

Zechel, David L.; Jochimsen, Bjarne

2014-01-01

SUMMARY After several decades of use of glyphosate, the active ingredient in weed killers such as Roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. Glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. This is in contrast to the general phosphorus compounds utilized and metabolized by microorganisms. Here phosphorus is found as phosphoric acid or phosphate ion, phosphoric acid esters, or phosphoric acid anhydrides. The latter compounds contain phosphorus that is bound only to oxygen. Hydrolytic, oxidative, and radical-based mechanisms for carbon-phosphorus bond cleavage have been described. This review deals with the radical-based mechanism employed by the carbon-phosphorus lyase of the carbon-phosphorus lyase pathway, which involves reactions for activation of phosphonate, carbon-phosphorus bond cleavage, and further chemical transformation before a useful phosphate ion is generated in a series of seven or eight enzyme-catalyzed reactions. The phn genes, encoding the enzymes for this pathway, are widespread among bacterial species. The processes are described with emphasis on glyphosate as a substrate. Additionally, the catabolism of glyphosate is intimately connected with that of aminomethylphosphonate, which is also treated in this review. Results of physiological and genetic analyses are combined with those of bioinformatics analyses. PMID:24600043

Modeling the effects of free-living marine bacterial community composition on heterotrophic remineralization rates and biogeochemical carbon cycling

NASA Astrophysics Data System (ADS)

Teel, E.; Liu, X.; Cram, J. A.; Sachdeva, R.; Fuhrman, J. A.; Levine, N. M.

2016-12-01

Global oceanic ecosystem models either disregard fluctuations in heterotrophic bacterial remineralization or vary remineralization as a simple function of temperature, available carbon, and nutrient limitation. Most of these models were developed before molecular techniques allowed for the description of microbial community composition and functional diversity. Here we investigate the impact of a dynamic heterotrophic community and variable remineralization rates on biogeochemical cycling. Specifically, we integrated variable microbial remineralization into an ecosystem model by utilizing molecular community composition data, association network analysis, and biogeochemical rate data from the San Pedro Ocean Time-series (SPOT) station. Fluctuations in free-living bacterial community function and composition were examined using monthly environmental and biological data collected at SPOT between 2000 and 2011. On average, the bacterial community showed predictable seasonal changes in community composition and peaked in abundance in the spring with a one-month lag from peak chlorophyll concentrations. Bacterial growth efficiency (BGE), estimated from bacterial production, was found to vary widely at the site (5% to 40%). In a multivariate analysis, 47.6% of BGE variability was predicted using primary production, bacterial community composition, and temperature. A classic Nutrient-Phytoplankton-Zooplankton-Detritus model was expanded to include a heterotroph module that captured the observed relationships at the SPOT site. Results show that the inclusion of dynamic bacterial remineralization into larger oceanic ecosystem models can significantly impact microzooplankton grazing, the duration of surface phytoplankton blooms, and picophytoplankton primary production rates.

Carbon nanotubes as cancer therapeutic carriers and mediators

PubMed Central

Son, Kuk Hui; Hong, Jeong Hee; Lee, Jin Woo

2016-01-01

Carbon nanotubes (CNTs) have received increasing attention in biomedical fields because of their unique structures and properties, including high aspect ratios, large surface areas, rich surface chemical functionalities, and size stability on the nanoscale. Particularly, they are attractive as carriers and mediators for cancer therapy. Through appropriate functionalization, CNTs have been used as nanocarriers for anticancer drugs including doxorubicin, camptothecin, carboplatin, cisplatin, paclitaxel, Pt(II), and Pt(IV), and genes including plasmid DNA, small-interfering RNA, oligonucleotides, and RNA/DNA aptamers. CNTs can also deliver proteins and immunotherapy components. Using combinations of light energy, they have also been applied as mediators for photothermal therapy and photodynamic therapy to directly destroy cancer cells without severely damaging normal tissue. If limitations such as a long-term cytotoxicity in the body, lack of size uniformity during the synthetic process, loading deviations for drug–CNT complexes, and release controllability at the target point are overcome, CNTs will become one of the strongest tools that are available for various other biomedical fields as well as for cancer therapy. PMID:27785021

Carbonic anhydrase enzymes regulate mast cell–mediated inflammation

PubMed Central

Soteropoulos, Patricia

2016-01-01

Type 2 cytokine responses are necessary for the development of protective immunity to helminth parasites but also cause the inflammation associated with allergies and asthma. Recent studies have found that peripheral hematopoietic progenitor cells contribute to type 2 cytokine–mediated inflammation through their enhanced ability to develop into mast cells. In this study, we show that carbonic anhydrase (Car) enzymes are up-regulated in type 2–associated progenitor cells and demonstrate that Car enzyme inhibition is sufficient to prevent mouse mast cell responses and inflammation after Trichinella spiralis infection or the induction of food allergy–like disease. Further, we used CRISPR/Cas9 technology and illustrate that genetically editing Car1 is sufficient to selectively reduce mast cell development. Finally, we demonstrate that Car enzymes can be targeted to prevent human mast cell development. Collectively, these experiments identify a previously unrecognized role for Car enzymes in regulating mast cell lineage commitment and suggest that Car enzyme inhibitors may possess therapeutic potential that can be used to treat mast cell–mediated inflammation. PMID:27526715

Postviral Complications: Bacterial Pneumonia.

PubMed

Prasso, Jason E; Deng, Jane C

2017-03-01

Secondary bacterial pneumonia after viral respiratory infection remains a significant source of morbidity and mortality. Susceptibility is mediated by a variety of viral and bacterial factors, and complex interactions with the host immune system. Prevention and treatment strategies are limited to influenza vaccination and antibiotics/antivirals respectively. Novel approaches to identifying the individuals with influenza who are at increased risk for secondary bacterial pneumonias are urgently needed. Given the threat of further pandemics and the heightened prevalence of these viruses, more research into the immunologic mechanisms of this disease is warranted with the hope of discovering new potential therapies. Published by Elsevier Inc.

Cryptic carbon and sulfur cycling between surface ocean plankton.

PubMed

Durham, Bryndan P; Sharma, Shalabh; Luo, Haiwei; Smith, Christa B; Amin, Shady A; Bender, Sara J; Dearth, Stephen P; Van Mooy, Benjamin A S; Campagna, Shawn R; Kujawinski, Elizabeth B; Armbrust, E Virginia; Moran, Mary Ann

2015-01-13

About half the carbon fixed by phytoplankton in the ocean is taken up and metabolized by marine bacteria, a transfer that is mediated through the seawater dissolved organic carbon (DOC) pool. The chemical complexity of marine DOC, along with a poor understanding of which compounds form the basis of trophic interactions between bacteria and phytoplankton, have impeded efforts to identify key currencies of this carbon cycle link. Here, we used transcriptional patterns in a bacterial-diatom model system based on vitamin B12 auxotrophy as a sensitive assay for metabolite exchange between marine plankton. The most highly up-regulated genes (up to 374-fold) by a marine Roseobacter clade bacterium when cocultured with the diatom Thalassiosira pseudonana were those encoding the transport and catabolism of 2,3-dihydroxypropane-1-sulfonate (DHPS). This compound has no currently recognized role in the marine microbial food web. As the genes for DHPS catabolism have limited distribution among bacterial taxa, T. pseudonana may use this sulfonate for targeted feeding of beneficial associates. Indeed, DHPS was both a major component of the T. pseudonana cytosol and an abundant microbial metabolite in a diatom bloom in the eastern North Pacific Ocean. Moreover, transcript analysis of the North Pacific samples provided evidence of DHPS catabolism by Roseobacter populations. Other such biogeochemically important metabolites may be common in the ocean but difficult to discriminate against the complex chemical background of seawater. Bacterial transformation of this diatom-derived sulfonate represents a previously unidentified and likely sizeable link in both the marine carbon and sulfur cycles.

Rapid and sensitive detection of Citrus Bacterial Canker by loop-mediated isothermal amplification combined with simple visual evaluation methods

PubMed Central

2010-01-01

Background Citrus Bacterial Canker (CBC) is a major, highly contagious disease of citrus plants present in many countries in Asia, Africa and America, but not in the Mediterranean area. There are three types of Citrus Bacterial Canker, named A, B, and C that have different genotypes and posses variation in host range within citrus species. The causative agent for type A CBC is Xanthomonas citri subsp. citri, while Xanthomonas fuscans subsp. aurantifolii, strain B causes type B CBC and Xanthomonas fuscans subsp. aurantifolii strain C causes CBC type C. The early and accurate identification of those bacteria is essential for the protection of the citrus industry. Detection methods based on bacterial isolation, antibodies or polymerase chain reaction (PCR) have been developed previously; however, these approaches may be time consuming, laborious and, in the case of PCR, it requires expensive laboratory equipment. Loop-mediated isothermal amplification (LAMP), which is a novel isothermal DNA amplification technique, is sensitive, specific, fast and requires no specialized laboratory equipment. Results A loop-mediated isothermal amplification assay for the diagnosis of Citrus Bacterial Canker (CBC-LAMP) was developed and evaluated. DNA samples were obtained from infected plants or cultured bacteria. A typical ladder-like pattern on gel electrophoresis was observed in all positive samples in contrast to the negative controls. In addition, amplification products were detected by visual inspection using SYBRGreen and using a lateral flow dipstick, eliminating the need for gel electrophoresis. The sensitivity and specificity of the assay were evaluated in different conditions and using several sample sources which included purified DNA, bacterium culture and infected plant tissue. The sensitivity of the CBC-LAMP was 10 fg of pure Xcc DNA, 5 CFU in culture samples and 18 CFU in samples of infected plant tissue. No cross reaction was observed with DNA of other phytopathogenic

Bacterial nitrogen fixation in sand bioreactors treating winery wastewater with a high carbon to nitrogen ratio.

PubMed

Welz, Pamela J; Ramond, Jean-Baptiste; Braun, Lorenz; Vikram, Surendra; Le Roes-Hill, Marilize

2018-02-01

Heterotrophic bacteria proliferate in organic-rich environments and systems containing sufficient essential nutrients. Nitrogen, phosphorus and potassium are the nutrients required in the highest concentrations. The ratio of carbon to nitrogen is an important consideration for wastewater bioremediation because insufficient nitrogen may result in decreased treatment efficiency. It has been shown that during the treatment of effluent from the pulp and paper industry, bacterial nitrogen fixation can supplement the nitrogen requirements of suspended growth systems. This study was conducted using physicochemical analyses and culture-dependent and -independent techniques to ascertain whether nitrogen-fixing bacteria were selected in biological sand filters used to treat synthetic winery wastewater with a high carbon to nitrogen ratio (193:1). The systems performed well, with the influent COD of 1351 mg/L being reduced by 84-89%. It was shown that the nitrogen fixing bacterial population was influenced by the presence of synthetic winery effluent in the surface layers of the biological sand filters, but not in the deeper layers. It was hypothesised that this was due to the greater availability of atmospheric nitrogen at the surface. The numbers of culture-able nitrogen-fixing bacteria, including presumptive Azotobacter spp. exhibited 1-2 log increases at the surface. The results of this study confirm that nitrogen fixation is an important mechanism to be considered during treatment of high carbon to nitrogen wastewater. If biological treatment systems can be operated to stimulate this phenomenon, it may obviate the need for nitrogen addition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Study of the Bioremediation of Atrazine under Variable Carbon and Nitrogen Sources by Mixed Bacterial Consortium Isolated from Corn Field Soil in Fars Province of Iran

PubMed Central

Nasseri, Simin; Hashemi, Hassan

2013-01-01

Atrazine herbicide that is widely used in corn production is frequently detected in water resources. The main objectives of this research were focused on assessing the effects of carbon and nitrogen sources on atrazine biodegradation by mixed bacterial consortium and by evaluating the feasibility of using mixed bacterial consortium in soil culture. Shiraz corn field soil with a long history of atrazine application has been explored for their potential of atrazine biodegradation. The influence of different carbon compounds and the effect of nitrogen sources and a different pH (5.5–8.5) on atrazine removal efficiency by mixed bacterial consortium in liquid culture were investigated. Sodium citrate and sucrose had the highest atrazine biodegradation rate (87.22%) among different carbon sources. Atrazine biodegradation rate decreased more quickly by the addition of urea (26.76%) compared to ammonium nitrate. Based on the data obtained in this study, pH of 7.0 is optimum for atrazine biodegradation. After 30 days of incubation, the percent of atrazine reduction rates were significantly enhanced in the inoculated soils (60.5%) as compared to uninoculated control soils (12%) at the soil moisture content of 25%. In conclusion, bioaugmentation of soil with mixed bacterial consortium may enhance the rate of atrazine degradation in a highly polluted soil. PMID:23533452

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

DOE PAGES

Staley, Christopher; Ferrieri, Abigail P.; Tfaily, Malak M.; ...

2017-06-24

The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.Significantly different bacterial community structures ( P = 0.031) were observed inmore » the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles.The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Staley, Christopher; Ferrieri, Abigail P.; Tfaily, Malak M.

The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.Significantly different bacterial community structures ( P = 0.031) were observed inmore » the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles.The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without

Direct and reversible hydrogenation of CO2 to formate by a bacterial carbon dioxide reductase.

PubMed

Schuchmann, K; Müller, V

2013-12-13

Storage and transportation of hydrogen is a major obstacle for its use as a fuel. An increasingly considered alternative for the direct handling of hydrogen is to use carbon dioxide (CO2) as an intermediate storage material. However, CO2 is thermodynamically stable, and developed chemical catalysts often require high temperatures, pressures, and/or additives for high catalytic rates. Here, we present the discovery of a bacterial hydrogen-dependent carbon dioxide reductase from Acetobacterium woodii directly catalyzing the hydrogenation of CO2. We also demonstrate a whole-cell system able to produce formate as the sole end product from dihydrogen (H2) and CO2 as well as syngas. This discovery opens biotechnological alternatives for efficient CO2 hydrogenation either by using the isolated enzyme or by employing whole-cell catalysis.

Development of a single-tube loop-mediated isothermal amplification assay for detection of four pathogens of bacterial meningitis.

PubMed

Huy, Nguyen Tien; Hang, Le Thi Thuy; Boamah, Daniel; Lan, Nguyen Thi Phuong; Van Thanh, Phan; Watanabe, Kiwao; Huong, Vu Thi Thu; Kikuchi, Mihoko; Ariyoshi, Koya; Morita, Kouichi; Hirayama, Kenji

2012-12-01

Several loop-mediated isothermal amplification (LAMP) assays have been developed to detect common causative pathogens of bacterial meningitis (BM). However, no LAMP assay is reported to detect Streptococcus agalactiae and Streptococcus suis, which are also among common pathogens of BM. Moreover, it is laborious and expensive by performing multiple reactions for each sample to detect bacterial pathogen. Thus, we aimed to design and develop a single-tube LAMP assay capable of detecting multiple bacterial species, based on the nucleotide sequences of the 16S rRNA genes of the bacteria. The nucleotide sequences of the 16S rRNA genes of main pathogens involved in BM were aligned to identify conserved regions, which were further used to design broad range specific LAMP assay primers. We successfully designed a set of broad range specific LAMP assay primers for simultaneous detection of four species including Staphylococcus aureus, Streptococcus pneumoniae, S. suis and S. agalactiae. The broad range LAMP assay was highly specific without cross-reactivity with other bacteria including Haemophilus influenzae, Neisseria meningitidis and Escherichia coli. The sensitivity of our LAMP assay was 100-1000 times higher compared with the conventional PCR assay. The bacterial species could be identified after digestion of the LAMP products with restriction endonuclease DdeI and HaeIII. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow.

PubMed

Zhang, Yuguang; Liu, Xiao; Cong, Jing; Lu, Hui; Sheng, Yuyu; Wang, Xiulei; Li, Diqiang; Liu, Xueduan; Yin, Huaqun; Zhou, Jizhong; Deng, Ye

2017-07-01

Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analysed using high-throughput technologies, including Illumina sequencing and geochip functional gene arrays. The soil microbial community structure and diversity were significantly (p < .05) different between alpine meadow and alpine steppe meadow; the microbial ɑ-diversity in alpine steppe meadow was significantly (p < .01) higher than in alpine meadow. Molecular ecological network analysis indicated that the microbial community structure in alpine steppe meadow was more complex and tighter than in the alpine meadow. The relative abundance of soil microbial labile carbon degradation genes (e.g., pectin and hemicellulose) was significantly higher in alpine steppe meadow than in alpine meadow, but the relative abundance of soil recalcitrant carbon degradation genes (e.g., chitin and lignin) showed the opposite tendency. The Biolog Ecoplate experiment showed that microbially mediated soil carbon utilization was more active in alpine steppe meadow than in alpine meadow. Consequently, more soil labile carbon might be decomposed in alpine steppe meadow than in alpine meadow. Therefore, the degenerative succession of alpine meadow because of climate change or anthropogenic activities would most likely decrease SOC and nutrients medicated by changing soil microbial community structure and their functional potentials for carbon decomposition. © 2017 John Wiley & Sons Ltd.

Empirical Leucine-to-Carbon Conversion Factors for Estimating Heterotrophic Bacterial Production: Seasonality and Predictability in a Temperate Coastal Ecosystem▿

PubMed Central

Calvo-Díaz, Alejandra; Morán, Xosé Anxelu G.

2009-01-01

Leucine-to-carbon conversion factors (CFs) are needed for converting substrate incorporation into biomass production of heterotrophic bacteria. During 2006 we performed 20 dilution experiments for determining the spatiotemporal variability of empirical CFs in temperate Atlantic coastal waters. Values (0.49 to 1.92 kg C mol Leu−1) showed maxima in autumn to early winter and minima in summer. Spatially averaged CFs were significantly negatively correlated with in situ leucine incorporation rates (r = −0.91) and positively correlated with phosphate concentrations (r = 0.76). These relationships, together with a strong positive covariation between cell-specific leucine incorporation rates and carbon contents (r = 0.85), were interpreted as a strategy to maximize survival through protein synthesis and low growth rates under nutrient limitation (low CFs) until favorable conditions stimulate cell division relative to protein synthesis (high CFs). A multiple regression with in situ leucine incorporation rates and cellular carbon contents explained 96% of CF variance in our ecosystem, suggesting their potential prediction from more easily measurable routine variables. The use of the theoretical CF of 1.55 kg C mol Leu−1 would have resulted in a serious overestimation (73%) of annual bacterial production rates. Our results emphasize the need for considering the temporal scale in CFs for bacterial production studies. PMID:19304821

Nitrate treatment effects on bacterial community biofilm formed on carbon steel in produced water stirred tank bioreactor.

PubMed

Marques, Joana Montezano; de Almeida, Fernando Pereira; Lins, Ulysses; Seldin, Lucy; Korenblum, Elisa

2012-06-01

To better understand the impact of nitrate in Brazilian oil reservoirs under souring processes and corrosion, the goal of this study was to analyse the effect of nitrate on bacterial biofilms formed on carbon steel coupons using reactors containing produced water from a Brazilian oil platform. Three independent experiments were carried out (E1, E2 and E3) using the same experimental conditions and different incubation times (5, 45 and 80 days, respectively). In every experiment, two biofilm-reactors were operated: one was treated with continuous nitrate flow (N reactor), and the other was a control reactor without nitrate (C reactor). A Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis approach using the 16S rRNA gene was performed to compare the bacterial groups involved in biofilm formation in the N and C reactors. DGGE profiles showed remarkable changes in community structure only in experiments E2 and E3. Five bands extracted from the gel that represented the predominant bacterial groups were identified as Bacillus aquimaris, B. licheniformis, Marinobacter sp., Stenotrophomonas maltophilia and Thioclava sp. A reduction in the sulfate-reducing bacteria (SRB) most probable number counts was observed only during the longer nitrate treatment (E3). Carbon steel coupons used for biofilm formation had a slightly higher weight loss in N reactors in all experiments. When the coupon surfaces were analysed by scanning electron microscopy, an increase in corrosion was observed in the N reactors compared with the C reactors. In conclusion, nitrate reduced the viable SRB counts. Nevertheless, the nitrate dosing increased the pitting of coupons.

Comparison between the evaluation of bacterial regrowth capability in a turbidimeter and biodegradable dissolved organic carbon bioreactor measurements in water.

PubMed

Kott, Y; Ribas, F; Frías, J; Lucena, F

1997-09-01

In recent years, two different approaches to the study of biodegradable organic matter in distribution systems have been followed. The assimilable organic carbon (AOC) indicates the portion of the dissolved organic matter used by bacteria and converted to biomass, which is directly measured as total bacteria, active bacteria or colony-forming units and indirectly as ATP or increase in turbidity. In contrast, the biodegradable dissolved organic carbon (BDOC) is the portion of the dissolved organic carbon that can be mineralized by heterotrophic microorganisms, and it is measured as the difference between the inflow and the outflow of a bioreactor. In this study, at different steps in a water treatment plant, the bacterial regrowth capability was determined by the AOC method that measures the maximum growth rate by using a computerized Monitek turbidimeter. The BDOC was determined using a plug flow bioreactor. Measurements of colony-forming units and total organic carbon (TOC) evolution in a turbidimeter and of colony-forming units at the inflow/outflow of the bioreactor were also performed, calculating at all sampling points the coefficient yield (Y = cfu/delta TOC) in both systems. The correlations between the results from the bioreactor and turbidimeter have been calculated; a high correlation level was observed between BDOC values and all the other parameters, except for Y calculated from bacterial suspension measured in the turbidimeter.

Interparticle interactions mediated superspin glass to superferromagnetic transition in Ni-bacterial cellulose aerogel nanocomposites

NASA Astrophysics Data System (ADS)

Thiruvengadam, V.; Vitta, Satish

2016-06-01

The interparticle interactions in the magnetic nanocomposites play a dominant role in controlling phase transitions: superparamagnetic to superspin glass and to superferromagnetic. These interactions can be tuned by controlling the size and number density of nanoparticles. The aerogel composites, 0.3Ni-BC and 0.7Ni-BC, consisting of Ni nanoparticles distributed in the bacterial cellulose have been used as a model system to study these interactions. Contrary to conventional approach, size of Ni-nanoparticles is not controlled and allowed to form naturally in bacterial cellulose template. The uncontrolled growth of Ni results in the formation of nanoparticles with 3 different size distributions - <10 nm particles along the length of fibrils, 50 nm particles in the intermediate spaces between the fibrils, and >100 nm particles in voids formed by reticulate structure. At room temperature, the composites exhibit a weakly ferromagnetic behaviour with a coercivity of 40 Oe, which increases to 160 Oe at 10 K. The transition from weakly ferromagnetic state to superferromagnetic state at low temperatures is mediated by the superspin glass state at intermediate temperatures via the interparticle interactions aided by nanoparticles present along the length of fibres. A temperature dependent microstructural model has been developed to understand the magnetic behaviour of nanocomposite aerogels.

Facile synthesis of carbon-mediated porous nanocrystallite anatase TiO2 for improved sodium insertion capabilities as an anode for sodium-ion batteries

NASA Astrophysics Data System (ADS)

Wu, Feng; Luo, Rui; Xie, Man; Li, Li; Zhang, Xiaoxiao; Zhao, Luzi; Zhou, Jiahui; Wang, KangKang; Chen, Renjie

2017-09-01

Porous carbon-mediated nanocrystallite anatase TiO2 composites are synthesized successfully via a simple dilatory hydrolysis-calcination method. The structural and morphological characterizations reveal that carbon-mediated TiO2 with a carbon content of 9.9 wt % (C2-TiO2) shows a combination of mesoporous and macroporous structures with a pore volume of 0.20 cm3 g-1 and surface area of 40.3 m2 g-1. Notably, C2-TiO2 delivered enhanced electrochemical performances of a high charge capacity of 259 mA h g-1 at 0.1 C and a high rate performance of 110 mA h g-1 after 150 cycles, even at 1 C. A significant decrease is also observed in the electrochemical impedance of the carbon-mediated samples, which explains superior electrochemical performance. Compared with the bare anatase TiO2 (B-TiO2), improved sodium storage capabilities of carbon-mediated samples are attributed to the participation of carbon to form a symbiotic structure with TiO2, which not only increases pore volume of the samples but serves as highly conductive network to provide a Na+ diffusion path during the insertion/de-insertion of sodium ions. All of these encouraging results suggest that carbon-mediated TiO2 has a great potential for improving sodium insertion capabilities with a facile and low-cost synthesis process.

Gene regulation mediates host specificity of a bacterial pathogen.

PubMed

Killiny, Nabil; Almeida, Rodrigo P P

2011-12-01

Many bacterial plant pathogens have a gene-for-gene relationship that determines host specificity. However, there are pathogens such as the xylem-limited bacterium Xylella fastidiosa that do not carry genes considered essential for the gene-for-gene model, such as those coding for a type III secretion system and effector molecules. Nevertheless, X. fastidiosa subspecies are host specific. A comparison of symptom development and host colonization after infection of plants with several mutant strains in two hosts, grapevines and almonds, indicated that X. fastidiosa virulence mechanisms are similar in those plants. Thus, we tested if modification of gene regulation patterns, by affecting the production of a cell-cell signalling molecule (DSF), impacted host specificity in X. fastidiosa. Results show that disruption of the rpfF locus, required for DSF synthesis, in a strain incapable of causing disease in grapevines, leads to symptom development in that host. These data are indicative that the core machinery required for the colonization of grapevines is present in that strain, and that changes in gene regulation alone can lead X. fastidiosa to exploit a novel host. The study of the evolution and mechanisms of host specificity mediated by gene regulation at the genome level could lead to important insights on the emergence of new diseases. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Nitrogen-doped carbon nanofibers derived from polypyrrole coated bacterial cellulose as high-performance electrode materials for supercapacitors and Li-ion batteries

DOE PAGES

Lei, Wen; Han, Lili; Xuan, Cuijuan; ...

2016-05-24

Here, nitrogen-doped carbon nanofiber (NDCN) was synthesized via carbonization of polypyrrole (PPy) coated bacterial cellulose (BC) composites, where BC serves as templates as well as precursor, and PPy serves as the nitrogen source. The synthesized NDCN was employed as electrode for both supercapacitors and Li-ion batteries. The large surface area exposed to electrolyte resulting from the 3D carbon networks leads to sufficient electrode/electrolyte interface and creates shorter transport paths of electrolyte ions and Li + ion. Besides, the three types of N dopants in NDCN improve the electronic conductivity, as well as superior electrochemical performance.

Curli mediate bacterial adhesion to fibronectin via tensile multiple bonds

NASA Astrophysics Data System (ADS)

Oh, Yoo Jin; Hubauer-Brenner, Michael; Gruber, Hermann J.; Cui, Yidan; Traxler, Lukas; Siligan, Christine; Park, Sungsu; Hinterdorfer, Peter

2016-09-01

Many enteric bacteria including pathogenic Escherichia coli and Salmonella strains produce curli fibers that bind to host surfaces, leading to bacterial internalization into host cells. By using a nanomechanical force-sensing approach, we obtained real-time information about the distribution of molecular bonds involved in the adhesion of curliated bacteria to fibronectin. We found that curliated E. coli and fibronectin formed dense quantized and multiple specific bonds with high tensile strength, resulting in tight bacterial binding. Nanomechanical recognition measurements revealed that approximately 10 bonds were disrupted either sequentially or simultaneously under force load. Thus the curli formation of bacterial surfaces leads to multi-bond structural components of fibrous nature, which may explain the strong mechanical binding of curliated bacteria to host cells and unveil the functions of these proteins in bacterial internalization and invasion.

Site-Specific Integration of Foreign DNA into Minimal Bacterial and Human Target Sequences Mediated by a Conjugative Relaxase

PubMed Central

Agúndez, Leticia; González-Prieto, Coral; Machón, Cristina; Llosa, Matxalen

2012-01-01

Background Bacterial conjugation is a mechanism for horizontal DNA transfer between bacteria which requires cell to cell contact, usually mediated by self-transmissible plasmids. A protein known as relaxase is responsible for the processing of DNA during bacterial conjugation. TrwC, the relaxase of conjugative plasmid R388, is also able to catalyze site-specific integration of the transferred DNA into a copy of its target, the origin of transfer (oriT), present in a recipient plasmid. This reaction confers TrwC a high biotechnological potential as a tool for genomic engineering. Methodology/Principal Findings We have characterized this reaction by conjugal mobilization of a suicide plasmid to a recipient cell with an oriT-containing plasmid, selecting for the cointegrates. Proteins TrwA and IHF enhanced integration frequency. TrwC could also catalyze integration when it is expressed from the recipient cell. Both Y18 and Y26 catalytic tyrosil residues were essential to perform the reaction, while TrwC DNA helicase activity was dispensable. The target DNA could be reduced to 17 bp encompassing TrwC nicking and binding sites. Two human genomic sequences resembling the 17 bp segment were accepted as targets for TrwC-mediated site-specific integration. TrwC could also integrate the incoming DNA molecule into an oriT copy present in the recipient chromosome. Conclusions/Significance The results support a model for TrwC-mediated site-specific integration. This reaction may allow R388 to integrate into the genome of non-permissive hosts upon conjugative transfer. Also, the ability to act on target sequences present in the human genome underscores the biotechnological potential of conjugative relaxase TrwC as a site-specific integrase for genomic modification of human cells. PMID:22292089

Bacterial and iron oxide aggregates mediate secondary iron mineral formation: green rust versus magnetite.

PubMed

Zegeye, A; Mustin, C; Jorand, F

2010-06-01

In the presence of methanoate as electron donor, Shewanella putrefaciens, a Gram-negative, facultative anaerobe, is able to transform lepidocrocite (gamma-FeOOH) to secondary Fe (II-III) minerals such as carbonated green rust (GR1) and magnetite. When bacterial cells were added to a gamma-FeOOH suspension, aggregates were produced consisting of both bacteria and gamma-FeOOH particles. Recently, we showed that the production of secondary minerals (GR1 vs. magnetite) was dependent on bacterial cell density and not only on iron reduction rates. Thus, gamma-FeOOH and S. putrefaciens aggregation pattern was suggested as the main mechanism driving mineralization. In this study, lepidocrocite bioreduction experiments, in the presence of anthraquinone disulfonate, were conducted by varying the [cell]/[lepidocrocite] ratio in order to determine whether different types of aggregate are formed, which may facilitate precipitation of GR1 as opposed to magnetite. Confocal laser scanning microscopy was used to analyze the relative cell surface area and lepidocrocite concentration within the aggregates and captured images were characterized by statistical methods for spatial data (i.e. variograms). These results suggest that the [cell]/[lepidocrocite] ratio influenced both the aggregate structure and the nature of the secondary iron mineral formed. Subsequently, a [cell]/[lepidocrocite] ratio above 1 x 10(7) cells mmol(-1) leads to densely packed aggregates and to the formation of GR1. Below this ratio, looser aggregates are formed and magnetite was systematically produced. The data presented in this study bring us closer to a more comprehensive understanding of the parameters governing the formation of minerals in dense bacterial suspensions and suggest that screening mineral-bacteria aggregate structure is critical to understanding (bio)mineralization pathways.

A comparative study on effects of heterotrophic microbial activity on the stability of bivalve and coral carbonate during early diagenesis.

NASA Astrophysics Data System (ADS)

Lange, Skadi M.; Krause, Stefan; Immenhauser, Adrian; Ritter, Ann-Christin; Gorb, Stanislav N.; Kleinteich, Thomas; Treude, Tina

2016-04-01

Following deposition and shallow burial, marine biogenic carbonates are exposed to an environment that is geochemically affected by a manifold of bacterial metabolic redox processes. To allow for comparison of potential microbe-mediated alteration effects on carbonates, we used aragonitic bivalve shell samples and porous aragonitic coral fragments for incubation experiments in oxic- and anoxic seawater media. The media contained marine sediment slurries or bacterial cultures to mimic the natural processes in vitro. The results for anoxic experimental media containing bivalve shell samples or coral fragments displayed considerable changes in carbonate-system parameters (pH, AT, CA, DIC) and divalent-cation ratios (Mg/Ca, Mg/Sr, Sr/Ca) over time. Furthermore, incubated bivalve shell samples were altered in morphology, elemental composition and isotopic signature. Coral-fragment bearing oxic incubations were run at two temperature regimes and divalent-cation ratios of the high-temperature bacterial medium displayed withdrawal of Ca2+ and Sr2+ from the medium, thus indicating microbe-induced secondary aragonite precipitation. Analyses of coral fragments include electron-microprobe mapping and X-ray microtomography to resolve elemental sample composition and pore-space alteration features, respectively. Up to this point our results indicate that heterotrophic bacterial activity has the potential to affect surficial or open pore space in carbonate archives by increasing rates of alteration relative to sterile environments.

Fermented milk containing Lactobacillus paracasei subsp. paracasei CNCM I-1518 reduces bacterial translocation in rats treated with carbon tetrachloride

PubMed Central

Sánchez, Elisabet; Nieto, Juan C.; Vidal, Silvia; Santiago, Alba; Martinez, Xavier; Sancho, Francesc J.; Sancho-Bru, Pau; Mirelis, Beatriz; Corominola, Helena; Juárez, Candido; Manichanh, Chaysavanh; Guarner, Carlos; Soriano, German

2017-01-01

Probiotics can prevent pathological bacterial translocation by modulating intestinal microbiota and improving the gut barrier. The aim was to evaluate the effect of a fermented milk containing Lactobacillus paracasei subsp. paracasei CNCM I-1518 on bacterial translocation in rats with carbon tetrachloride (CCl4)-induced cirrhosis. Sprague-Dawley rats treated with CCl4 were randomized into a probiotic group that received fermented milk containing Lactobacillus paracasei subsp. paracasei CNCM I-1518 in drinking water or a water group that received water only. Laparotomy was performed one week after ascites development. We evaluated bacterial translocation, intestinal microbiota, the intestinal barrier and cytokines in mesenteric lymph nodes and serum. Bacterial translocation decreased and gut dysbiosis improved in the probiotic group compared to the water group. The ileal β-defensin-1 concentration was higher and ileal malondialdehyde levels were lower in the probiotic group than in water group. There were no differences between groups in serum cytokines but TNF-α levels in mesenteric lymph nodes were lower in the probiotic group than in the water group. Fermented milk containing Lactobacillus paracasei subsp. paracasei CNCM I-1518 decreases bacterial translocation, gut dysbiosis and ileal oxidative damage and increases ileal β-defensin-1 expression in rats treated with CCl4, suggesting an improvement in the intestinal barrier integrity. PMID:28368023

Calcium carbonate mineralization mediated by in vitro cultured mantle cells from Pinctada fucata.

PubMed

Kong, Wei; Li, Shiguo; Xiang, Liang; Xie, Liping; Zhang, Rongqing

2015-08-07

Formation of the molluscan shell is believed to be an extracellular event mediated by matrix proteins. We report calcium carbonate mineralization mediated by Pinctada fucata mantle cells. Crystals only appeared when mantle cells were present in the crystallization solution. These crystals were piled up in highly ordered units and showed the typical characteristics of biomineralization products. A thin organic framework was observed after dissolving the crystals in EDTA. Some crystals had etched surfaces with a much smoother appearance than other parts. Mantle cells were observed to be attached to some of these smooth surfaces. These results suggest that mantle cells may be directly involved in the nucleation and remodeling process of calcium carbonate mineralization. Our result demonstrate the practicability of studying the mantle cell mechanism of biomineralization and contribute to the overall understanding of the shell formation process. Copyright © 2015 Elsevier Inc. All rights reserved.

Bacterial production in the water column of small streams highly depends on terrestrial dissolved organic carbon

NASA Astrophysics Data System (ADS)

Graeber, Daniel; Poulsen, Jane R.; Rasmussen, Jes J.; Kronvang, Brian; Zak, Dominik; Kamjunke, Norbert

2016-04-01

In the recent years it has become clear that the largest part of the terrestrial dissolved organic carbon (DOC) pool is removed on the way from the land to the ocean. Yet it is still unclear, where in the freshwater systems terrestrial DOC is actually taken up, and for streams DOC uptake was assumed to happen mostly at the stream bottom (benthic zone). However, a recent monitoring study implies that water column but not benthic bacteria are strongly affected by the amount and composition of DOM entering streams from the terrestrial zone. We conducted an experiment to compare the reaction of the bacterial production and heterotrophic uptake in the water column and the benthic zone to a standardized source of terrestrial DOC (leaf leachate from Beech litter). In detail, we sampled gravel and water from eight streams with a gradient in stream size and land use. For each stream four different treatments were incubated at 16°C for three days and each stream: filtered stream water with gravel stones (representing benthic zone bacteria) or unfiltered stream water (representing water column bacteria), both either with (n = 5) or, without (n = 3) leaf leachate. We found that the bacterial uptake of leaf litter DOC was higher for the benthic zone likely due to the higher bacterial production compared to the water column. In contrast, the bacterial production per amount of leaf leachate DOC taken up was significantly higher for the bacteria in the water column than for those in the benthic zone. This clearly indicates a higher growth efficiency with the leaf leachate DOC for the bacteria in the water column than in the benthic zone. We found a high variability for the growth efficiency in the water column, which was best explained by a negative correlation of the DOC demand with stream width (R² = 0.86, linear correlation of log-transformed data). This was not the case for the benthic zone bacteria (R² = 0.02). This implies that water column bacteria in very small streams

Plant-bacterial pathogen interactions mediated by type III effectors.

PubMed

Feng, Feng; Zhou, Jian-Min

2012-08-01

Effectors secreted by the bacterial type III system play a central role in the interaction between Gram-negative bacterial pathogens and their host plants. Recent advances in the effector studies have helped cementing several key concepts concerning bacterial pathogenesis, plant immunity, and plant-pathogen co-evolution. Type III effectors use a variety of biochemical mechanisms to target specific host proteins or DNA for pathogenesis. The identifications of their host targets led to the identification of novel components of plant innate immune system. Key modules of plant immune signaling pathways such as immune receptor complexes and MAPK cascades have emerged as a major battle ground for host-pathogen adaptation. These modules are attacked by multiple type III effectors, and some components of these modules have evolved to actively sense the effectors and trigger immunity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bacterial magnetic particles improve testes-mediated transgene efficiency in mice.

PubMed

Wang, Chao; Sun, Guanghong; Wang, Ye; Kong, Nana; Chi, Yafei; Yang, Leilei; Xin, Qiliang; Teng, Zhen; Wang, Xu; Wen, Yujun; Li, Ying; Xia, Guoliang

2017-11-01

Nano-scaled materials have been proved to be ideal DNA carriers for transgene. Bacterial magnetic particles (BMPs) help to reduce the toxicity of polyethylenimine (PEI), an efficient gene-transferring agent, and assist tissue transgene ex vivo. Here, the effectiveness of the BMP-PEI complex-conjugated foreign DNAs (BPDs) in promoting testes-mediated gene transfer (TMGT) in mouse was compared with that of liposome-conjugated foreign DNAs. The results proved that through testes injection, the clusters of BPDs successfully reached the cytoplasm and the nuclear of spermatogenesis cell, and expressed in testes of transgene founder mice. Additionally, the ratio of founder mice obtained from BPDs (88%) is about 3 times higher than the control (25%) (p < 0.05). Interestingly, the motility of sperms recovered from epididymis of the founder mice from BPD group were significantly improved, as compared with the control (p < 0.01). Based on classic breeding, the ratio of transgene mice within the first filial was significantly higher in BPDs compared with the control (73.8% versus 11.6%, p < 0.05). TMGT in this study did not produce visible histological changes in the testis. In conclusion, nano-scaled BPDs could be an alternative strategy for efficiently producing transgene mice in vivo.

Production of bacterial cellulose using different carbon sources and culture media.

PubMed

Mohammadkazemi, Faranak; Azin, Mehrdad; Ashori, Alireza

2015-03-06

In this work, the effects of carbon sources and culture media on the production and structural properties of bacterial cellulose (BC) have been studied. BC nanofibers were synthesized using Gluconacetobacter xylinus strain PTCC 1734. Media used were Hestrin-Schramm (H), Yamanaka (Y), and Zhou (Z). Five different carbon sources, namely date syrup, glucose, mannitol, sucrose, and food-grade sucrose were used in these media. All the produced BC pellicles were characterized in terms of dry weight production, biomass yield, thermal stability, crystallinity and morphology by thermogravimetric analysis (TGA), x-ray diffraction (XRD), and field emission scanning electron microscopy (FE-SEM). The obtained results showed that mannitol lead to the highest yield, followed by sucrose. The highest production efficiency of mannitol might be due to the nitrogen source, which plays an important role. The maximum improvement on the thermal stability of the composites was achieved when mannitol was used in H medium. In addition, the crystallinity was higher in BC formed in H medium compared to other media. FE-SEM micrographs illustrated that the BC pellicles, synthesized in the culture media H and Z, were stable, unlike those in medium Y that were unstable. The micrographs of BC produced in media containing mannitol and sucrose provided evidence of the strong interfacial adhesion between the BC fibers without noticeable aggregates. Copyright © 2014 Elsevier Ltd. All rights reserved.

Differing Daphnia magna assimilation efficiencies for terrestrial, bacterial, and algal carbon and fatty acids.

PubMed

Taipale, Sami J; Brett, Michael T; Hahn, Martin W; Martin-Creuzburg, Dominik; Yeung, Sean; Hiltunen, Minna; Strandberg, Ursula; Kankaala, Paula

2014-02-01

There is considerable interest in the pathways by which carbon and growth-limiting elemental and biochemical nutrients are supplied to upper trophic levels. Fatty acids and sterols are among the most important molecules transferred across the plant-animal interface of food webs. In lake ecosystems, in addition to phytoplankton, bacteria and terrestrial organic matter are potential trophic resources for zooplankton, especially in those receiving high terrestrial organic matter inputs. We therefore tested carbon, nitrogen, and fatty acid assimilation by the crustacean Daphnia magna when consuming these resources. We fed Daphnia with monospecific diets of high-quality (Cryptomonas marssonii) and intermediate-quality (Chlamydomonas sp. and Scenedesmus gracilis) phytoplankton species, two heterotrophic bacterial strains, and particles from the globally dispersed riparian grass, Phragmites australis, representing terrestrial particulate organic carbon (t-POC). We also fed Daphnia with various mixed diets, and compared Daphnia fatty acid, carbon, and nitrogen assimilation across treatments. Our results suggest that bacteria were nutritionally inadequate diets because they lacked sterols and polyunsaturated omega-3 and omega-6 (omega-3 and omega-6) fatty acids (PUFAs). However, Daphnia were able to effectively use carbon and nitrogen from Actinobacteria, if their basal needs for essential fatty acids and sterols were met by phytoplankton. In contrast to bacteria, t-POC contained sterols and omega-6 and omega-3 fatty acids, but only at 22%, 1.4%, and 0.2% of phytoplankton levels, respectively, which indicated that t-POC food quality was especially restricted with regard to omega-3 PUFAs. Our results also showed higher assimilation of carbon than fatty acids from t-POC and bacteria into Daphnia, based on stable-isotope and fatty acids analysis, respectively. A relatively high (>20%) assimilation of carbon and fatty acids from t-POC was observed only when the proportion of t

Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity--a large-scale system analysis of decoded bacterial genomes.

PubMed

Shestov, Maksim; Ontañón, Santiago; Tozeren, Aydin

2015-10-13

Bacterial infections comprise a global health challenge as the incidences of antibiotic resistance increase. Pathogenic potential of bacteria has been shown to be context dependent, varying in response to environment and even within the strains of the same genus. We used the KEGG repository and extensive literature searches to identify among the 2527 bacterial genomes in the literature those implicated as pathogenic to the host, including those which show pathogenicity in a context dependent manner. Using data on the gene contents of these genomes, we identified sets of genes highly abundant in pathogenic but relatively absent in commensal strains and vice versa. In addition, we carried out genome comparison within a genus for the seventeen largest genera in our genome collection. We projected the resultant lists of ortholog genes onto KEGG bacterial pathways to identify clusters and circuits, which can be linked to either pathogenicity or synergy. Gene circuits relatively abundant in nonpathogenic bacteria often mediated biosynthesis of antibiotics. Other synergy-linked circuits reduced drug-induced toxicity. Pathogen-abundant gene circuits included modules in one-carbon folate, two-component system, type-3 secretion system, and peptidoglycan biosynthesis. Antibiotics-resistant bacterial strains possessed genes modulating phagocytosis, vesicle trafficking, cytoskeletal reorganization, and regulation of the inflammatory response. Our study also identified bacterial genera containing a circuit, elements of which were previously linked to Alzheimer's disease. Present study produces for the first time, a signature, in the form of a robust list of gene circuitry whose presence or absence could potentially define the pathogenicity of a microbiome. Extensive literature search substantiated a bulk majority of the commensal and pathogenic circuitry in our predicted list. Scanning microbiome libraries for these circuitry motifs will provide further insights into the complex

Simultaneous biodegradation of phenol and carbon tetrachloride mediated by humic acids.

PubMed

Martínez, Claudia M; Alvarez, Luis H; Cervantes, Francisco J

2012-09-01

The capacity of an anaerobic sediment to achieve the simultaneous biodegradation of phenol and carbon tetrachloride (CT) was evaluated, using humic acids (HA) as redox mediator. The presence of HA in sediment incubations increased the rate of biodegradation of phenol and the rate of dehalogenation (2.5-fold) of CT compared to controls lacking HA. Further experiments revealed that the electron-accepting capacity of HA derived from different organic-rich environments was not associated with their reducing capacity to achieve CT dechlorination. The collected kinetic data suggest that the reduction of CT by reduced HA was the rate-limiting step during the simultaneous biodegradation of phenol and CT. To our knowledge, the present study constitutes the first demonstration of the simultaneous biodegradation of two priority pollutants mediated by HA.

Key Issues Concerning Biolog Use for Aerobic and Anaerobic Freshwater Bacterial Community-Level Physiological Profiling

NASA Astrophysics Data System (ADS)

Christian, Bradley W.; Lind, Owen T.

2006-06-01

Bacterial heterotrophy in aquatic ecosystems is important in the overall carbon cycle. Biolog MicroPlates provide information into the metabolic potential of bacteria involved in carbon cycling. Specifically, Biolog EcoPlatesTM were developed with ecologically relevant carbon substrates to allow investigators to measure carbon substrate utilization patterns and develop community-level physiological profiles from natural bacterial assemblages. However, understanding of the functionality of these plates in freshwater research is limited. We explored several issues of EcoPlate use for freshwater bacterial assemblages including inoculum density, incubation temperature, non-bacterial color development, and substrate selectivity. Each of these has various effects on plate interpretation. We offer suggestions and techniques to resolve these interpretation issues. Lastly we propose a technique to allow EcoPlate use in anaerobic freshwater bacterial studies.

Survival of selected bacterial species in sterilized activated carbon filters and biological activated carbon filters.

PubMed Central

Rollinger, Y; Dott, W

1987-01-01

The survival of selected hygienically relevant bacterial species in activated carbon (AC) filters on a bench scale was investigated. The results revealed that after inoculation of the test strains the previously sterilized AC absorbed all bacteria (10(6) to 10(7)). After a period of 6 to 13 days without countable bacteria in the effluent, the numbers of Escherichia coli, Pseudomonas aeruginosa, and Pseudomonas putida increased up to 10(4) to 10(5) CFU/ml of effluent and 10(6) to 10(7) CFU/g of AC. When Klebsiella pneumoniae and Streptococcus faecalis were used, no growth in filters could be observed. The numbers of E. coli, P. aeruginosa, and P. putida, however, decreased immediately and showed no regrowth in nonsterile AC from a filter which had been continuously connected to running tap water for 2 months. Under these conditions an autochthonous microflora developed on the carbon surface which could be demonstrated by scanning electron microscopy and culturing methods (heterotrophic plate count). These bacteria reduced E. coli, P. aeruginosa, and P. putida densities in the effluent by a factor of more than 10(5) within 1 to 5 days. The hypothesis that antagonistic substances of the autochthonous microflora were responsible for the elimination of the artificial contamination could not be confirmed because less than 1% of the isolates of the autochthonous microflora were able to produce such substances as indicated by in vitro tests. Competition for limiting nutrients was thought to be the reason for the observed effects. PMID:3579281

A family of conserved bacterial effectors inhibits salicylic acid-mediated basal immunity and promotes disease necrosis in plants.

PubMed

DebRoy, Sruti; Thilmony, Roger; Kwack, Yong-Bum; Nomura, Kinya; He, Sheng Yang

2004-06-29

Salicylic acid (SA)-mediated host immunity plays a central role in combating microbial pathogens in plants. Inactivation of SA-mediated immunity, therefore, would be a critical step in the evolution of a successful plant pathogen. It is known that mutations in conserved effector loci (CEL) in the plant pathogens Pseudomonas syringae (the Delta CEL mutation), Erwinia amylovora (the dspA/E mutation), and Pantoea stewartii subsp. stewartii (the wtsE mutation) exert particularly strong negative effects on bacterial virulence in their host plants by unknown mechanisms. We found that the loss of virulence in Delta CEL and dspA/E mutants was linked to their inability to suppress cell wall-based defenses and to cause normal disease necrosis in Arabidopsis and apple host plants. The Delta CEL mutant activated SA-dependent callose deposition in wild-type Arabidopsis but failed to elicit high levels of callose-associated defense in Arabidopsis plants blocked in SA accumulation or synthesis. This mutant also multiplied more aggressively in SA-deficient plants than in wild-type plants. The hopPtoM and avrE genes in the CEL of P. syringae were found to encode suppressors of this SA-dependent basal defense. The widespread conservation of the HopPtoM and AvrE families of effectors in various bacteria suggests that suppression of SA-dependent basal immunity and promotion of host cell death are important virulence strategies for bacterial infection of plants.

Assembling the bacterial segrosome.

PubMed

Hayes, Finbarr; Barillà, Daniela

2006-05-01

Genome segregation in prokaryotes is a highly ordered process that integrates with DNA replication, cytokinesis and other fundamental facets of the bacterial cell cycle. The segrosome is the nucleoprotein complex that mediates DNA segregation in bacteria, its assembly and organization is best understood for plasmid partition. The recent elucidation of structures of the ParB plasmid segregation protein bound to centromeric DNA, and of the tertiary structures of other segregation proteins, are key milestones in the path to deciphering the molecular basis of bacterial DNA segregation.

Bacterially mediated diagenetic origin for chert-hosted manganese deposits in the Franciscan Complex, California Coast Ranges

NASA Astrophysics Data System (ADS)

Hein, James R.; Koski, Randolph A.

1987-08-01

Numerous manganese deposits in the Franciscan Complex, California, occur as conformable lenses within bedded radiolarian chert-argillite sequences that are, in turn, intercalated within thicker sections of sandstone and shale. The field relations, composition, and petro-graphic and isotopic characteristics indicate that the manganese was concentrated by diagenetic reconstitution of siliceous and hemipelagic sediment during burial. The ore lenses are Mn-rich and Fe-poor assemblages consisting largely of rhodochrosite, manganese silicates, opal-CT (disordered cristobalite-tridymite), and quartz. Highly negative δ13C values for the carbonate carbon in rhodochrosite indicate that CO2 likely originated from oxidation of methane; less negative values result from mixing of methanogenic carbon and CO2 derived from bacterial degradation of organic matter. The δ18O values for the carbonate of rhodochrosite indicate temperatures of formation between 12 and 100 °C. The oxidation of methane prior to carbonate precipitation may have used the minor (0.4% 0.5%) Mn and Fe oxyhydroxides and oxides deposited with the sediment. The mobilization of manganese from biogenic and terrigenous sources in the sediment column into discrete horizons and the fractioriation of manganese from iron reflect the presence of oxidation-reduction boundaries and gradients in the sediment column. Fluids derived from compaction and silica-dehydration reactions in the transformation of opal-A (X-ray amorphous biogenic silica) to quartz were involved in transportation of principal components. Sedimentary and geochemical attributes suggest that the deposits formed in a deep-water environment in a zone of oceanic upwelling near a continental margin.

Distinct Cellular Locations of Carbonic Anhydrases Mediate Carbon Dioxide Control of Stomatal Movements1[OPEN

PubMed Central

Hu, Honghong; Rappel, Wouter-Jan; Occhipinti, Rossana; Ries, Amber; Böhmer, Maik; You, Lei; Xiao, Chuanlei; Engineer, Cawas B.; Boron, Walter F.; Schroeder, Julian I.

2015-01-01

Elevated carbon dioxide (CO2) in leaves closes stomatal apertures. Research has shown key functions of the β-carbonic anhydrases (βCA1 and βCA4) in rapid CO2-induced stomatal movements by catalytic transmission of the CO2 signal in guard cells. However, the underlying mechanisms remain unclear, because initial studies indicate that these Arabidopsis (Arabidopsis thaliana) βCAs are targeted to distinct intracellular compartments upon expression in tobacco (Nicotiana benthamiana) cells. Which cellular location of these enzymes plays a key role in native guard cells in CO2-regulated stomatal movements remains unknown. Here, we express fluorescently tagged CAs in guard cells of ca1ca4 double-mutant plants and show that the specific locations of βCA4 at the plasma membrane and βCA1 in native guard cell chloroplasts each can mediate rapid CO2 control of stomatal movements. Localization and complementation analyses using a mammalian αCAII-yellow fluorescent protein in guard cells further show that cytoplasmic localization is also sufficient to restore CO2 regulation of stomatal conductance. Mathematical modeling of cellular CO2 catalysis suggests that the dynamics of the intracellular HCO3− concentration change in guard cells can be driven by plasma membrane and cytoplasmic localizations of CAs but not as clearly by chloroplast targeting. Moreover, modeling supports the notion that the intracellular HCO3− concentration dynamics in guard cells are a key mechanism in mediating CO2-regulated stomatal movements but that an additional chloroplast role of CAs exists that has yet to be identified. PMID:26243620

Impact of titanium dioxide nanoparticles on the bacterial communities of biological activated carbon filter intended for drinking water treatment.

PubMed

Zhiyuan, Liu; Shuili, Yu; Heedeung, Park; Qingbin, Yuan; Guicai, Liu; Qi, Li

2016-08-01

Titanium dioxide nanoparticles (TiO2 NPs) are inevitably present in the aquatic environment owing to their increasing production and use. However, knowledge of the potential effects of TiO2 NPs on the treatment of drinking water is scarce. Herein, the effects of two types of anatase TiO2 NPs (TP1, 25 nm; TP2, 100 nm) on the bacterial community in a biological activated carbon (BAC) filter were investigated via quantitative polymerase chain reaction (Q-PCR) analysis, ATP quantification, and 454 pyrosequencing analysis. Both TP1 and TP2 significantly inhibited the bacterial ATP level (p < 0.01) and induced a decrease in the abundance of bacterial 16S rDNA gene copies at doses of 0.1 and 100 mg L(-1). Simultaneously, the diversity and evenness of the bacterial communities were considerably reduced. The relative abundances of bacteria annotated to OTUs from Nitrospira class and Betaproteobacteria class decreased upon TiO2 NP treatment, whereas those of Bacilli class and Gammaproteobacteria class increased. TiO2 NP size showed a greater effect on the bacterial composition than did the dose based on Bray-Curtis distances. These findings identified negative effects of TiO2 NPs on the bacterial community in the BAC filter. Given the fact that BAC filters are used widely in drinking water treatment plants, these results suggested a potential threat by TiO2 NP to drinking water treatment system.

Adaptation of the neutral bacterial comet assay to assess antimicrobial-mediated DNA double-strand breaks in Escherichia coli

PubMed Central

SOLANKY, DIPESH; HAYDEL, SHELLEY E.

2012-01-01

This study aimed to determine the mechanism of action of a natural antibacterial clay mineral mixture, designated CB, by investigating the induction of DNA double-strand breaks (DSBs) in Escherichia coli. To quantify DNA damage upon exposure to soluble antimicrobial compounds, we modified a bacterial neutral comet assay, which primarily associates the general length of an electrophoresed chromosome, or comet, with the degree of DSB-associated DNA damage. To appropriately account for antimicrobial-mediated strand fragmentation, suitable control reactions consisting of exposures to water, ethanol, kanamycin, and bleomycin were developed and optimized for the assay. Bacterial exposure to the CB clay resulted in significantly longer comet lengths, compared to water and kanamycin exposures, suggesting that the induction of DNA DSBs contributes to the killing activity of this antibacterial clay mineral mixture. The comet assay protocol described herein provides a general technique for evaluating soluble antimicrobial-derived DNA damage and for comparing DNA fragmentation between experimental and control assays. PMID:22940101

Inhibition of bacterial growth in sweet cheese whey by carbon dioxide as determined by culture-independent community profiling.

PubMed

Lo, Raquel; Xue, Tian; Weeks, Mike; Turner, Mark S; Bansal, Nidhi

2016-01-18

Whey is a valuable co-product from cheese making that serves as a raw material for a wide range of products. Its rich nutritional content lends itself to rapid spoilage, thus it typically needs to be pasteurised and refrigerated promptly. Despite the extensive literature on milk spoilage bacteria, little is known about the spoilage bacteria of whey. The utility of carbon dioxide (CO2) to extend the shelf-life of raw milk and cottage cheese has been well established, but its application in whey preservation has not yet been explored. This study aims to characterise the microbial populations of fresh and spoiled sweet whey by culture-independent community profiling using 454 pyrosequencing of 16S rRNA gene amplicons and to determine whether carbonation is effective in inhibiting bacterial growth in sweet whey. The microbiota of raw Cheddar and Mozzarella whey was dominated by cheese starter bacteria. After pasteurisation, two out of the three samples studied became dominated by diverse environmental bacteria from various phyla, with Proteobacteria being the most dominant. Diverse microbial profiles were maintained until spoilage occurred, when the entire population was dominated by just one or two genera. Whey spoilage bacteria were found to be similar to those of milk. Pasteurised Cheddar and Mozzarella whey was spoiled by Bacillus sp. or Pseudomonas sp., and raw Mozzarella whey was spoiled by Pseudomonas sp., Serratia sp., and other members of the Enterobacteriaceae family. CO2 was effective in inhibiting bacterial growth of pasteurised Cheddar and Mozzarella whey stored at 15°C and raw Mozzarella whey stored at 4°C. The spoilage bacteria of the carbonated samples were similar to those of the non-carbonated controls. Copyright © 2015 Elsevier B.V. All rights reserved.

Macroporous graphitic carbon foam decorated with polydopamine as a high-performance anode for microbial fuel cell

NASA Astrophysics Data System (ADS)

Jiang, Hongmei; Yang, Lu; Deng, Wenfang; Tan, Yueming; Xie, Qingji

2017-09-01

Herein, a macroporous graphitic carbon foam (MGCF) electrode decorated with polydopamine (PDA) is used as a high-performance anode for microbial fuel cell (MFC) applications. The MGCF is facilely prepared by pyrolysis of a powder mixture comprising maltose, nickel nitrate, and ammonia chloride, without using solid porous template. The MGCF is coated with PDA by self-polymerization of dopamine in a basic solution. The MGCF can provide a large surface area for bacterial attachment, and PDA coated on the MGCF electrode can further promote bacterial adhesion resulting from the improved hydrophility, so the MGCF-PDA electrode as an anode in a MFC can show ultrahigh bacterial loading capacity. Moreover, the electrochemical oxidation of flavins at the MGCF-PDA electrode is greatly accelerated, so the extracellular electron transfer mediated by flavins is improved. As a result, the MFC equipped with a MGCF-PDA anode can show a maximum power density of 1735 mW cm-2, which is 6.7 times that of a MFC equipped with a commercial carbon felt anode, indicating a promising anode for MFC applications.

Bacillus megaterium mediated mineralization of calcium carbonate as biogenic surface treatment of green building materials.

PubMed

Dhami, Navdeep Kaur; Reddy, M Sudhakara; Mukherjee, Abhijit

2013-12-01

Microbially induced calcium carbonate precipitation is a biomineralization process that has various applications in remediation and restoration of range of building materials. In the present study, calcifying bacteria, Bacillus megaterium SS3 isolated from calcareous soil was applied as biosealant to enhance the durability of low energy, green building materials (soil-cement blocks). This bacterial isolate produced high amounts of urease, carbonic anhydrase, extra polymeric substances and biofilm. The calcium carbonate polymorphs produced by B. megaterium SS3 were analyzed by scanning electron microscopy, confocal laser scanning microscopy, X-ray diffraction and Fourier transmission infra red spectroscopy. These results suggested that calcite is the most predominant carbonate formed by this bacteria followed by vaterite. Application of B. megaterium SS3 as biogenic surface treatment led to 40 % decrease in water absorption, 31 % decrease in porosity and 18 % increase in compressive strength of low energy building materials. From the present investigation, it is clear that surface treatment of building materials by B. megaterium SS3 is very effective and eco friendly way of biodeposition of coherent carbonates that enhances the durability of building materials.

Characterization of bacterial community and iron corrosion in drinking water distribution systems with O3-biological activated carbon treatment.

PubMed

Xing, Xueci; Wang, Haibo; Hu, Chun; Liu, Lizhong

2018-07-01

Bacterial community structure and iron corrosion were investigated for simulated drinking water distribution systems (DWDSs) composed of annular reactors incorporating three different treatments: ozone, biologically activated carbon and chlorination (O 3 -BAC-Cl 2 ); ozone and chlorination (O 3 -Cl 2 ); or chlorination alone (Cl 2 ). The lowest corrosion rate and iron release, along with more Fe 3 O 4 formation, occurred in DWDSs with O 3 -BAC-Cl 2 compared to those without a BAC filter. It was verified that O 3 -BAC influenced the bacterial community greatly to promote the relative advantage of nitrate-reducing bacteria (NRB) in DWDSs. Moreover, the advantaged NRB induced active Fe(III) reduction coupled to Fe(II) oxidation, enhancing Fe 3 O 4 formation and inhibiting corrosion. In addition, O 3 -BAC pretreatment could reduce high-molecular-weight fractions of dissolved organic carbon effectively to promote iron particle aggregation and inhibit further iron release. Our findings indicated that the O 3 -BAC treatment, besides removing organic pollutants in water, was also a good approach for controlling cast iron corrosion and iron release in DWDSs. Copyright © 2017. Published by Elsevier B.V.

Dual functional nisin-multi-walled carbon nanotubes coated filters for bacterial capture and inactivation.

PubMed

Dong, Xiuli; Yang, Liju

2015-01-01

Removal of pathogens from water is one way to prevent waterborne illness. In this paper, we developed dual functional carbon nanotube (CNT) modified filters for bacterial capture and inactivation, utilizing multi-walled CNTs (MWCNTs) to coat on commercially available filters and making use of the exceptional adsorption property of CNTs to adsorb a natural antimicrobial peptide-nisin on it. Two types of MWCNTs with different outer layer diameters were used (MWCNTs1: <8 nm in diameter; MWCNTs2: 10-20 nm in diameter). The thickness of MWCNT layers, surface morphology, and surface hydrophobicity of both types of MWCNT coated filters were characterized. The MWCNT coating on filters significantly increased the surface hydrophobicity. The absorption of nisin and the capture of bacterial pathogens were correlated with increased surface hydrophobicity. The MWCNTs1 and MWCNTs2 filters with 1.5 mg MWCNTs loading captured 2.44 and 3.88 log of cells, respectively, from aqueous solutions containing a total of ~10(6) CFU/mL cells. Nisin deposit at the amount of 0.5 mg on the surfaces of MWCNT filters significantly reduced the viability of captured B. anthracis cells by 95.71-97.19 %, and inhibited the metabolic activities of the captured cells by approximately 98.3 %. The results demonstrated that the MWCNT-nisin filters achieved dual functions in bacterial pathogen capture and inhibition in one single filtration step, which is potentially applicable in removing undesired microorganisms from water sources and inhibiting captured Gram positive bacteria activities.

Proteome analysis of Arabidopsis seedlings exposed to bacterial volatiles.

PubMed

Kwon, Young Sang; Ryu, Choong-Min; Lee, Soohyun; Park, Hyo Bee; Han, Ki Soo; Lee, Jung Han; Lee, Kyunghee; Chung, Woo Sik; Jeong, Mi-Jeong; Kim, Hee Kyu; Bae, Dong-Won

2010-11-01

Plant root-associated bacteria (rhizobacteria) elicit plant basal immunity referred to as induced systemic resistance (ISR) against multiple pathogens. Among multi-bacterial determinants involving such ISR, the induction of ISR and promotion of growth by bacterial volatile compounds was previously reported. To exploit global de novo expression of plant proteins by bacterial volatiles, proteomic analysis was performed after exposure of Arabidopsis plants to the rhizobacterium Bacillus subtilis GB03. Ethylene biosynthesis enzymes were significantly up-regulated. Analysis by quantitative reverse transcriptase polymerase chain reaction confirmed that ethylene biosynthesis-related genes SAM-2, ACS4, ACS12, and ACO2 as well as ethylene response genes, ERF1, GST2, and CHIB were up-regulated by the exposure to bacterial volatiles. More interestingly, the emission of bacterial volatiles significantly up-regulated both key defense mechanisms mediated by jasmonic acid and salicylic acid signaling pathways. In addition, high accumulation of antioxidant proteins also provided evidence of decreased sensitivity to reactive oxygen species during the elicitation of ISR by bacterial volatiles. The present results suggest that the proteomic analysis of plant defense responses in bacterial volatile-mediated ISR can reveal the mechanisms of plant basal defenses orchestrated by endogenous ethylene production pathways and the generation of reactive oxygen species.

Carbon nanotubes/carbon fiber hybrid material: a super support material for sludge biofilms.

PubMed

Liu, Qijie; Dai, Guangze; Bao, Yanling

2017-07-16

Carbon fiber (CF) is widely used as a sludge biofilm support material for wastewater treatment. Carbon nanotubes/carbon fiber (CNTs/CF) hybrid material was prepared by ultrasonically assisted electrophoretic deposition (EPD). CF supports (CF without handling, CF oxidized by nitric acid, CNTs/CF hybrid material) were evaluated by sludge immobilization tests, bacterial cell adsorption tests and Derjaguin -Landau -Verwey -Overbeek (DLVO) theory. We found that the CNTs/CF hybrid material has a high capacity for adsorbing activated sludge, nitrifying bacterial sludge and pure strains (Escherichia coli and Staphylococcus aureus). CNTs deposited on CF surface easily wound around the curved surface of bacterial cell which resulted in capturing more bacterial cells. DLVO theory indicated the lowest total interaction energy of CNTs/CF hybrid material, which resulted in the highest bacteria cell adsorption velocity. Experiments and DLVO theory results proved that CNTs/CF hybrid material is a super support material for sludge biofilms.

Disequilibrium δ18O values in microbial carbonates as a tracer of metabolic production of dissolved inorganic carbon

NASA Astrophysics Data System (ADS)

Thaler, Caroline; Millo, Christian; Ader, Magali; Chaduteau, Carine; Guyot, François; Ménez, Bénédicte

2017-02-01

Carbon and oxygen stable isotope compositions of carbonates are widely used to retrieve paleoenvironmental information. However, bias may exist in such reconstructions as carbonate precipitation is often associated with biological activity. Several skeleton-forming eukaryotes have been shown to precipitate carbonates with significant offsets from isotopic equilibrium with water. Although poorly understood, the origin of these biologically-induced isotopic shifts in biogenic carbonates, commonly referred to as "vital effects", could be related to metabolic effects that may not be restricted to mineralizing eukaryotes. The aim of our study was to determine whether microbially-mediated carbonate precipitation can also produce offsets from equilibrium for oxygen isotopes. We present here δ18O values of calcium carbonates formed by the activity of Sporosarcina pasteurii, a carbonatogenic bacterium whose ureolytic activity produces ammonia (thus increasing pH) and dissolved inorganic carbon (DIC) that precipitates as solid carbonates in the presence of Ca2+. We show that the 1000 lnαCaCO3-H2O values for these bacterially-precipitated carbonates are up to 24.7‰ smaller than those expected for precipitation at isotopic equilibrium. A similar experiment run in the presence of carbonic anhydrase (an enzyme able to accelerate oxygen isotope equilibration between DIC and water) resulted in δ18O values of microbial carbonates in line with values expected at isotopic equilibrium with water. These results demonstrate for the first time that bacteria can induce calcium carbonate precipitation in strong oxygen isotope disequilibrium with water, similarly to what is observed for eukaryotes. This disequilibrium effect can be unambiguously ascribed to oxygen isotope disequilibrium between DIC and water inherited from the oxygen isotope composition of the ureolytically produced CO2, probably combined with a kinetic isotope effect during CO2 hydration/hydroxylation. The fact that

Hydrologically mediated iron reduction/oxidation fluctuations and dissolved organic carbon exports in tidal wetlands

NASA Astrophysics Data System (ADS)

Guimond, J. A.; Seyfferth, A.; Michael, H. A.

2017-12-01

Salt marshes are biogeochemical hotspots where large quantities of carbon are processed and stored. High primary productivity and deposition of carbon-laden sediment enable salt marsh soils to accumulate and store organic carbon. Conversely, salt marshes can laterally export carbon from the marsh platform to the tidal channel and eventually the ocean via tidal pumping. However, carbon export studies largely focus on tidal channels, missing key physical and biogeochemical mechanisms driving the mobilization of dissolved organic carbon (DOC) within the marsh platform and limiting our understanding of and ability to predict coastal carbon dynamics. We hypothesize that iron redox dynamics mediate the mobilization/immobilization of DOC in the top 30 cm of salt marsh sediment near tidal channels. The mobilized DOC can then diffuse into the flooded surface water or be advected to tidal channels. To elucidate DOC dynamics driven by iron redox cycles, we measured porewater DOC, Fe(II), total iron, total sulfate, pH, redox potential, and electrical conductivity (EC) beside the creek, at the marsh levee, and in the marsh interior in a mid-latitude tidal salt marsh in Dover, Delaware. Samples were collected at multiple tide stages during a spring and neap tide at depths of 5-75cm. Samples were also collected from the tidal channel. Continuous Eh measurements were made using in-situ electrodes. A prior study shows that DOC and Fe(II) concentrations vary spatially across the marsh. Redox conditions near the creek are affected by tidal oscillations. High tides saturate the soil and decrease redox potential, whereas at low tide, oxygen enters the sediment and increases the Eh. This pattern is always seen in the top 7-10cm of sediment, with more constant low Eh at depth. However, during neap tides, this signal penetrates deeper. Thus, between the creek and marsh levee, hydrology mediates redox conditions. Based on porewater chemistry, if DOC mobilization can be linked to redox

Effect of Different Carbon Sources on Bacterial Nanocellulose Production and Structure Using the Low pH Resistant Strain Komagataeibacter Medellinensis

PubMed Central

Molina-Ramírez, Carlos; Castro, Margarita; Osorio, Marlon; Torres-Taborda, Mabel; Gómez, Beatriz; Zuluaga, Robin; Gómez, Catalina; Gañán, Piedad; Rojas, Orlando J.; Castro, Cristina

2017-01-01

Bacterial cellulose (BC) is a polymer obtained by fermentation with microorganism of different genera. Recently, new producer species have been discovered, which require identification of the most important variables affecting cellulose production. In this work, the influence of different carbon sources in BC production by a novel low pH-resistant strain Komagataeibacter medellinensis was established. The Hestrin-Schramm culture medium was used as a reference and was compared to other media comprising glucose, fructose, and sucrose, used as carbon sources at three concentrations (1, 2, and 3% w/v). The BC yield and dynamics of carbon consumption were determined at given fermentation times during cellulose production. While the carbon source did not influence the BC structural characteristics, different production levels were determined: glucose > sucrose > fructose. These results highlight considerations to improve BC industrial production and to establish the BC property space for applications in different fields. PMID:28773001

Two decades of warming increases diversity of a potentially lignolytic bacterial community

PubMed Central

Pold, Grace; Melillo, Jerry M.; DeAngelis, Kristen M.

2015-01-01

As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming. PMID:26042112

Bacterially-mediated precipitation of ferric iron during the leaching of basaltic rocks

NASA Astrophysics Data System (ADS)

Schnittker, K.; Navarrete, J. U.; Cappelle, I. J.; Borrok, D. M.

2011-12-01

The bacterially-mediated oxidation of ferrous [Fe(II)] iron in environments where its oxidation is otherwise unfavorable (i.e., acidic and/or anaerobic conditions) results in the formation of ferric iron [Fe(III)] precipitates. The mineralogy and morphologies of these precipitates are dictated by solution biochemistry. In this study, we evaluated Fe(III) precipitates that formed during aerobic bioleaching experiments with Acidithiobacillus ferrooxidans and ilmenite (FeTiO3) and Lunar or Martian basaltic stimulant rocks. Growth media was supplied to support the bacteria; however, all the Fe(II) for chemical energy was supplied by the mineral or rock. During the experiments, the bacteria actively oxidized Fe(II) to Fe(III), resulting in the formation of white and yellow-colored precipitates. In our initial experiments with both ilmentite and basalt, High-Resolution Scanning Electron Microscopic (HRSEM) analysis indicated that the precipitates where small (diameters were less than 5μm and mostly nanometer-scaled), white, and exhibited a platy texture. Networks of mineralized bacterial biofilm were also abundant. In these cases the white precipitates coated the bacteria, forming rod-shaped minerals 5-10μm long by about 1μm in diameter. Many of the rod-shaped minerals formed elongated chains. Energy Dispersive Spectra (EDS) analysis showed that the precipitates were largely composed of Fe and phosphorous (P) with an atomic Fe:P ratio of ˜1. Limited sulfur (S) was also identified as part of the agglomerated precipitates with an atomic Fe:S ratio that ranged from 5 to 10. Phosphorous and S were introduced into the system in considerable amounts as part of the growth media. Additional experiments were performed where we altered the growth media to lower the amount of available P by an order of magnitude. In this case, the experimental behavior remained the same, but the precipitates were more yellow or orange in color relative to those in the experiments using the

Diversity and Biomineralization Potential of the Epilithic Bacterial Communities Inhabiting the Oldest Public Stone Monument of Cluj-Napoca (Transylvania, Romania)

PubMed Central

Andrei, Adrian-Ştefan; Păuşan, Manuela R.; Tămaş, Tudor; Har, Nicolae; Barbu-Tudoran, Lucian; Leopold, Nicolae; Banciu, Horia L.

2017-01-01

In this study, we investigated the biomineralization potential and diversity of the epilithic bacterial communities dwelling on the limestone statue of Saint Donatus, the oldest public monument of Cluj-Napoca city (Transylvania region, NW Romania). Their spatial distribution together with phylogenetic and metabolic diversity, as well as their capacity to precipitate calcium carbonate was evaluated by combining molecular and phenotypic fingerprinting methods with X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron-microscopy analyses. The results of real-time quantitative PCR, molecular fingerprinting and community-level physiological profiling showed that diverse and abundant bacterial assemblages that differ in relation to their collection site colonized the statue. The cultivation and molecular identification procedures allowed the characterization of 79 bacterial isolates belonging to Proteobacteria (73.4%), Firmicutes (19%), and Actinobacteria (7.6%). Amongst them, the 22 strains identified as being capable of calcium carbonate precipitation were found to belong mostly to Bacillus and Pseudomonas genera. We found that bacteria acted as nucleation sites, inducing the formation of nanoscale aggregates that were shown to be principally composed of vaterite. Furthermore, we expanded the current knowledge on culturable diversity of carbonatogenic bacteria by providing evidence for biogenic vaterite/calcite formation mediated by: Pseudomonas synxantha, P. graminis, Brevibacterium iodinum, Streptomyces albidoflavus, and Stenotrophomonas chelatiphaga. Overall, this study highlights the need to evaluate the carbonatogenetic potential of all the bacterial communities present on stone artwork prior to designing an efficient conservation treatment based on biomineralization. PMID:28326074

Measurements of carbon utilization by single bacterial species in sterile soil: insights into Rhizobium spp.

PubMed

Wigley, K; Wakelin, S A; Moot, D J; Hammond, S; Ridgway, H J

2016-08-01

The aim of this work was to develop a tool to investigate the influence of soil factors on carbon utilization activity of single micro-organisms. The assay for Rhizobium leguminosarum bv. trifolii in γ-irradiated soil, using the MicroResp(™) system, was optimized for sterility, incubation time, and moisture level. The optimized method was validated with experiments that assessed (i) differences in C utilization of different rhizobia strains and (ii) how this was affected by soil type. Carbon utilization differed among strains of the same species (and symbiovar), but some strains were more responsive to the soil environment than others. This novel modification of the MicroResp(™) has enabled the scope of carbon-utilization patterns of single strains of bacteria, such as Rh. leguminosarum bv. trifolii, to be studied in soil. The system is a new tool with applications in microbial ecology adaptable to the study of many culturable bacterial and fungal soil-borne taxa. It will allow measurement of a micro-organism's ability to utilize common C sources released in rhizosphere exudates to be measured in a physical soil background. This knowledge may improve selection efficiency and deployment of commercial microbial inoculants. © 2016 The Society for Applied Microbiology.

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed.

PubMed

Song, Liyan; Li, Lei

2016-08-01

Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a

Maresin 1, a Proresolving Lipid Mediator, Mitigates Carbon Tetrachloride-Induced Liver Injury in Mice

PubMed Central

Li, Ruidong; Wang, Yaxin; Zhao, Ende; Wu, Ke; Li, Wei; Shi, Liang; Wang, Di; Xie, Gengchen; Yin, Yuping; Deng, Meizhou; Zhang, Peng; Tao, Kaixiong

2016-01-01

Maresin 1 (MaR 1) was recently reported to have protective properties in several different animal models of acute inflammation by inhibiting inflammatory response. However, its function in acute liver injury is still unknown. To address this question, we induced liver injury in BALB/c mice with intraperitoneal injection of carbon tetrachloride with or without treatment of MaR 1. Our data showed that MaR 1 attenuated hepatic injury, oxidative stress, and lipid peroxidation induced by carbon tetrachloride, as evidenced by increased thiobarbituric acid reactive substances and reactive oxygen species levels were inhibited by treatment of MaR 1. Furthermore, MaR 1 increased activities of antioxidative mediators in carbon tetrachloride-treated mice liver. MaR 1 decreased indices of inflammatory mediators such as tumor necrosis factor-α, interleukin-6, interleukin-1β, monocyte chemotactic protein 1, myeloperoxidase, cyclooxygenase-2, and inducible nitric oxide synthase. Administration of MaR 1 inhibited activation of nuclear factor kappa B (NF-κb) and mitogen-activated protein kinases (MAPKs) in the liver of CCl4 treated mice. In conclusion, these results suggested the antioxidative, anti-inflammatory properties of MaR 1 in CCl4 induced liver injury. The possible mechanism is partly implicated in its abilities to inhibit ROS generation and activation of NF-κb and MAPK pathway. PMID:26881046

Bacterial Cellulose: A Robust Platform for Design of Three Dimensional Carbon-Based Functional Nanomaterials.

PubMed

Wu, Zhen-Yu; Liang, Hai-Wei; Chen, Li-Feng; Hu, Bi-Cheng; Yu, Shu-Hong

2016-01-19

Three dimensional (3D) carbon nanomaterials exhibit great application potential in environmental protection, electrochemical energy storage and conversion, catalysis, polymer science, and advanced sensors fields. Current methods for preparing 3D carbon nanomaterials, for example, carbonization of organogels, chemical vapor deposition, and self-assembly of nanocarbon building blocks, inevitably involve some drawbacks, such as expensive and toxic precursors, complex equipment and technological requirements, and low production ability. From the viewpoint of practical application, it is highly desirable to develop a simple, cheap, and environmentally friendly way for fabricating 3D carbon nanomaterials in large scale. On the other hand, in order to extend the application scope and improve the performance of 3D carbon nanomaterials, we should explore efficient strategies to prepare diverse functional nanomaterials based on their 3D carbon structure. Recently, many researchers tend to fabricate high-performance 3D carbon-based nanomaterials from biomass, which is low cost, easy to obtain, and nontoxic to humans. Bacterial cellulose (BC), a typical biomass material, has long been used as the raw material of nata-de-coco (an indigenous dessert food of the Philippines). It consists of a polysaccharide with a β-1,4-glycosidic linkage and has a interconnected 3D porous network structure. Interestingly, the network is made up of a random assembly of cellulose nanofibers, which have a high aspect ratio with a diameter of 20-100 nm. As a result, BC has a high specific surface area. Additionally, BC hydrogels can be produced on an industrial scale via a microbial fermentation process at a very low price. Thus, it can be an ideal platform for design of 3D carbon-based functional nanomaterials. Before our work, no systematic work and summary on this topic had been reported. This Account presents the concepts and strategies of our studies on BC in the past few years, that is

Rapid bacterial mineralization of organic carbon produced during a phytoplankton bloom induced by natural iron fertilization in the Southern Ocean

NASA Astrophysics Data System (ADS)

Obernosterer, Ingrid; Christaki, Urania; Lefèvre, Dominique; Catala, Philippe; Van Wambeke, France; Lebaron, Philippe

2008-03-01

The response of heterotrophic bacteria ( Bacteria and Archaea) to the spring phytoplankton bloom that occurs annually above the Kerguelen Plateau (Southern Ocean) due to natural iron fertilization was investigated during the KErguelen Ocean and Plateau compared Study (KEOPS) cruise in January-February 2005. In surface waters (upper 100 m) in the core of the phytoplankton bloom, heterotrophic bacteria were, on an average, 3-fold more abundant and revealed rates of production ([ 3H] leucine incorporation) and respiration (<0.8 μm size fraction) that exceeded those in surrounding high-nutrient low-chlorophyll (HNLC) waters by factors of 6 and 5, respectively. These differences in bacterial metabolic activities were attributable to high-nucleic-acid-containing cells that dominated (≈80% of total cell abundance) the heterotrophic bacterial community associated with the phytoplankton bloom. Bacterial growth efficiencies varied between 14% and 20% inside the bloom and were <10% in HNLC waters. Results from bottle-incubation experiments performed at the bloom station indicated that iron had no direct but an indirect effect on heterotrophic bacterial activity, due to the stimulation by phytoplankton-derived dissolved organic matter. Within the Kerguelen bloom, bacterial carbon demand accounted for roughly 45% of gross community production. These results indicate that heterotrophic bacteria processed a significant portion of primary production, with most of it being rapidly respired.

Bacterial plasmid-mediated quinolone resistance genes in aquatic environments in China

PubMed Central

Yan, Lei; Liu, Dan; Wang, Xin-Hua; Wang, Yunkun; Zhang, Bo; Wang, Mingyu; Xu, Hai

2017-01-01

Emerging antimicrobial resistance is a major threat to human’s health in the 21st century. Understanding and combating this issue requires a full and unbiased assessment of the current status on the prevalence of antimicrobial resistance genes and their correlation with each other and bacterial groups. In aquatic environments that are known reservoirs for antimicrobial resistance genes, we were able to reach this goal on plasmid-mediated quinolone resistance (PMQR) genes that lead to resistance to quinolones and possibly also to the co-emergence of resistance to β-lactams. Novel findings were made that qepA and aac-(6′)-Ib genes that were previously regarded as similarly abundant with qnr genes are now dominant among PMQR genes in aquatic environments. Further statistical analysis suggested that the correlation between PMQR and β-lactam resistance genes in the environment is still weak, that the correlations between antimicrobial resistance genes could be weakened by sufficient wastewater treatment, and that the prevalence of PMQR has been implicated in environmental, pathogenic, predatory, anaerobic, and more importantly, human symbiotic bacteria. This work provides a comprehensive analysis of PMQR genes in aquatic environments in Jinan, China, and provides information with which combat with the antimicrobial resistance problem may be fought. PMID:28094345

Enhanced Disease Susceptibility1 Mediates Pathogen Resistance and Virulence Function of a Bacterial Effector in Soybean1[C][W][OPEN

PubMed Central

Wang, Jialin; Shine, M.B.; Gao, Qing-Ming; Navarre, Duroy; Jiang, Wei; Liu, Chunyan; Chen, Qingshan; Hu, Guohua; Kachroo, Aardra

2014-01-01

Enhanced disease susceptibility1 (EDS1) and phytoalexin deficient4 (PAD4) are well-known regulators of both basal and resistance (R) protein-mediated plant defense. We identified two EDS1-like (GmEDS1a/GmEDS1b) proteins and one PAD4-like (GmPAD4) protein that are required for resistance signaling in soybean (Glycine max). Consistent with their significant structural conservation to Arabidopsis (Arabidopsis thaliana) counterparts, constitutive expression of GmEDS1 or GmPAD4 complemented the pathogen resistance defects of Arabidopsis eds1 and pad4 mutants, respectively. Interestingly, however, the GmEDS1 and GmPAD4 did not complement pathogen-inducible salicylic acid accumulation in the eds1/pad4 mutants. Furthermore, the GmEDS1a/GmEDS1b proteins were unable to complement the turnip crinkle virus coat protein-mediated activation of the Arabidopsis R protein Hypersensitive reaction to Turnip crinkle virus (HRT), even though both interacted with HRT. Silencing GmEDS1a/GmEDS1b or GmPAD4 reduced basal and pathogen-inducible salicylic acid accumulation and enhanced soybean susceptibility to virulent pathogens. The GmEDS1a/GmEDS1b and GmPAD4 genes were also required for Resistance to Pseudomonas syringae pv glycinea2 (Rpg2)-mediated resistance to Pseudomonas syringae. Notably, the GmEDS1a/GmEDS1b proteins interacted with the cognate bacterial effector AvrA1 and were required for its virulence function in rpg2 plants. Together, these results show that despite significant structural similarities, conserved defense signaling components from diverse plants can differ in their functionalities. In addition, we demonstrate a role for GmEDS1 in regulating the virulence function of a bacterial effector. PMID:24872380

Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces.

PubMed

Franzetti, Andrea; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Minora, Umberto; Mayer, Christoph; Azzoni, Roberto S; Diolaiuti, Guglielmina; Smiraglia, Claudio; Ambrosini, Roberto

2016-12-01

Biological processes on glacier surfaces affect glacier reflectance, influence surface energy budget and glacier response to climate warming, and determine glacier carbon exchange with the atmosphere. Currently, carbon balance of supraglacial environment is assessed as the balance between the activity of oxygenic phototrophs and the respiration rate of heterotrophic organisms. Here we present a metagenomic analysis of tiny wind-blown supraglacial sediment (cryoconite) from Baltoro (Pakistani Karakoram) and Forni (Italian Alps) glaciers, providing evidence for the occurrence in these environments of different and previously neglected metabolic pathways. Indeed, we observed high abundance of heterotrophic anoxygenic phototrophs, suggesting that light might directly supplement the energy demand of some bacterial strains allowing them to use as carbon source organic molecules, which otherwise would be respired. Furthermore, data suggest that CO 2 could be produced also by microbiologically mediated oxidation of CO, which may be produced by photodegradation of organic matter.

A repeatedly refuelable mediated biofuel cell based on a hierarchical porous carbon electrode

NASA Astrophysics Data System (ADS)

Fujita, Shuji; Yamanoi, Shun; Murata, Kenichi; Mita, Hiroki; Samukawa, Tsunetoshi; Nakagawa, Takaaki; Sakai, Hideki; Tokita, Yuichi

2014-05-01

Biofuel cells that generate electricity from renewable fuels, such as carbohydrates, must be reusable through repeated refuelling, should these devices be used in consumer electronics. We demonstrate the stable generation of electricity from a glucose-powered mediated biofuel cell through multiple refuelling cycles. This refuelability is achieved by immobilizing nicotinamide adenine dinucleotide (NAD), an electron-transfer mediator, and redox enzymes in high concentrations on porous carbon particles constituting an anode while maintaining their electrochemical and enzymatic activities after the immobilization. This bioanode can be refuelled continuously for more than 60 cycles at 1.5 mA cm-2 without significant potential drop. Cells assembled with these bioanodes and bilirubin-oxidase-based biocathodes can be repeatedly used to power a portable music player at 1 mW cm-3 through 10 refuelling cycles. This study suggests that the refuelability within consumer electronics should facilitate the development of long and repeated use of the mediated biofuel cells as well as of NAD-based biosensors, bioreactors, and clinical applications.

Voltammetric determination of homocysteine using multiwall carbon nanotube paste electrode in the presence of chlorpromazine as a mediator.

PubMed

Gholami-Orimi, Fathali; Taleshi, Farshad; Biparva, Pourya; Karimi-Maleh, Hassan; Beitollahi, Hadi; Ebrahimi, Hamid R; Shamshiri, Mohamad; Bagheri, Hasan; Fouladgar, Masoud; Taherkhani, Ali

2012-01-01

We propose chlorpromazine (CHP) as a new mediator for the rapid, sensitive, and highly selective voltammetric determination of homocysteine (Hcy) using multiwall carbon nanotube paste electrode (MWCNTPE). The experimental results showed that the carbon nanotube paste electrode has a highly electrocatalytic activity for the oxidation of Hcy in the presence of CHP as a mediator. Cyclic voltammetry, double potential step chronoamperometry, and square wave voltammetry (SWV) are used to investigate the suitability of CHP at the surface of MWCNTPE as a mediator for the electrocatalytic oxidation of Hcy in aqueous solutions. The kinetic parameters of the system, including electron transfer coefficient, and catalytic rate constant were also determined using the electrochemical approaches. In addition, SWV was used for quantitative analysis. SWV showed wide linear dynamic range (0.1-210.0 μM Hcy) with a detection limit of 0.08 μM Hcy. Finally, this method was also examined as a selective, simple, and precise electrochemical sensor for the determination of Hcy in real samples.

Exposure of Bacterial Biofilms to Electrical Current Leads to Cell Death Mediated in Part by Reactive Oxygen Species

PubMed Central

Brinkman, Cassandra L.; Schmidt-Malan, Suzannah M.; Karau, Melissa J.; Greenwood-Quaintance, Kerryl; Hassett, Daniel J.; Mandrekar, Jayawant N.

2016-01-01

Bacterial biofilms may form on indwelling medical devices such as prosthetic joints, heart valves and catheters, causing challenging-to-treat infections. We have previously described the ‘electricidal effect’, in which bacterial biofilms are decreased following exposure to direct electrical current. Herein, we sought to determine if the decreased bacterial quantities are due to detachment of biofilms or cell death and to investigate the role that reactive oxygen species (ROS) play in the observed effect. Using confocal and electron microscopy and flow cytometry, we found that direct current (DC) leads to cell death and changes in the architecture of biofilms formed by Gram-positive and Gram-negative bacteria. Reactive oxygen species (ROS) appear to play a role in DC-associated cell death, as there was an increase in ROS-production by Staphylococcus aureus and Staphylococcus epidermidis biofilms following exposure to DC. An increase in the production of ROS response enzymes catalase and superoxide dismutase (SOD) was observed for S. aureus, S. epidermidis and Pseudomonas aeruginosa biofilms following exposure to DC. Additionally, biofilms were protected from cell death when supplemented with antioxidants and oxidant scavengers, including catalase, mannitol and Tempol. Knocking out SOD (sodAB) in P. aeruginosa led to an enhanced DC effect. Microarray analysis of P. aeruginosa PAO1 showed transcriptional changes in genes related to the stress response and cell death. In conclusion, the electricidal effect results in death of bacteria in biofilms, mediated, at least in part, by production of ROS. PMID:27992529

Exposure of Bacterial Biofilms to Electrical Current Leads to Cell Death Mediated in Part by Reactive Oxygen Species.

PubMed

Brinkman, Cassandra L; Schmidt-Malan, Suzannah M; Karau, Melissa J; Greenwood-Quaintance, Kerryl; Hassett, Daniel J; Mandrekar, Jayawant N; Patel, Robin

2016-01-01

Bacterial biofilms may form on indwelling medical devices such as prosthetic joints, heart valves and catheters, causing challenging-to-treat infections. We have previously described the 'electricidal effect', in which bacterial biofilms are decreased following exposure to direct electrical current. Herein, we sought to determine if the decreased bacterial quantities are due to detachment of biofilms or cell death and to investigate the role that reactive oxygen species (ROS) play in the observed effect. Using confocal and electron microscopy and flow cytometry, we found that direct current (DC) leads to cell death and changes in the architecture of biofilms formed by Gram-positive and Gram-negative bacteria. Reactive oxygen species (ROS) appear to play a role in DC-associated cell death, as there was an increase in ROS-production by Staphylococcus aureus and Staphylococcus epidermidis biofilms following exposure to DC. An increase in the production of ROS response enzymes catalase and superoxide dismutase (SOD) was observed for S. aureus, S. epidermidis and Pseudomonas aeruginosa biofilms following exposure to DC. Additionally, biofilms were protected from cell death when supplemented with antioxidants and oxidant scavengers, including catalase, mannitol and Tempol. Knocking out SOD (sodAB) in P. aeruginosa led to an enhanced DC effect. Microarray analysis of P. aeruginosa PAO1 showed transcriptional changes in genes related to the stress response and cell death. In conclusion, the electricidal effect results in death of bacteria in biofilms, mediated, at least in part, by production of ROS.

New insights on the baker's yeast-mediated hydration of oleic acid: the bacterial contaminants of yeast are responsible for the stereoselective formation of (R)-10-hydroxystearic acid.

PubMed

Serra, S; De Simeis, D

2018-03-01

The preparation of the high-value flavour γ-dodecalactone is based on the biotransformation of natural 10-HSA, which is in turn obtained by microbial hydration of oleic acid. We want to establish a reliable baker's yeast-mediated procedure for 10-HSA preparation. The previously reported yeast-mediated hydration procedures are unreliable because bacteria-free baker's yeast is not able to hydrate oleic acid. The actual responsible for performing this reaction are the bacterial contaminants present in baker's yeast. Moreover, we demonstrated that the enantioselectivity in the production of (R)-10-HSA is affected mainly by the temperature used in the biotransformation. We demonstrated that Saccharomyces cerevisiae is not able to hydrate oleic acid, whereas different bacterial strains present in baker's yeast transform oleic acid into (R)-10-HSA. We reported a general procedure for the preparation of (R)-10-HSA starting from oleic acid and using commercially available baker's yeast. This study holds both scientific and industrial interest. It unambiguously establishes that the eukaryote micro-organisms present in baker's yeast are not able to hydrate oleic acid. The isolation of oleic acid hydrating bacterial strains from commercial baker's yeast points to their prospective use for the industrial synthesis of 10-HSA. © 2017 The Society for Applied Microbiology.

An olfactory subsystem that detects carbon disulfide and mediates food-related social learning.

PubMed

Munger, Steven D; Leinders-Zufall, Trese; McDougall, Lisa M; Cockerham, Renee E; Schmid, Andreas; Wandernoth, Petra; Wennemuth, Gunther; Biel, Martin; Zufall, Frank; Kelliher, Kevin R

2010-08-24

Olfactory signals influence social interactions in a variety of species. In mammals, pheromones and other social cues can promote mating or aggression behaviors; can communicate information about social hierarchies, genetic identity and health status; and can contribute to associative learning. However, the molecular, cellular, and neural mechanisms underlying many olfactory-mediated social interactions remain poorly understood. Here, we report that a specialized olfactory subsystem that includes olfactory sensory neurons (OSNs) expressing the receptor guanylyl cyclase GC-D, the cyclic nucleotide-gated channel subunit CNGA3, and the carbonic anhydrase isoform CAII (GC-D(+) OSNs) is required for the acquisition of socially transmitted food preferences (STFPs) in mice. Using electrophysiological recordings from gene-targeted mice, we show that GC-D(+) OSNs are highly sensitive to the volatile semiochemical carbon disulfide (CS(2)), a component of rodent breath and a known social signal mediating the acquisition of STFPs. Olfactory responses to CS(2) are drastically reduced in mice lacking GC-D, CNGA3, or CAII. Disruption of this sensory transduction cascade also results in a failure to acquire STFPs from either live or surrogate demonstrator mice or to exhibit hippocampal correlates of STFP retrieval. Our findings indicate that GC-D(+) OSNs detect chemosignals that facilitate food-related social interactions. Copyright 2010 Elsevier Ltd. All rights reserved.

Radical-Mediated Enzymatic Carbon Chain Fragmentation-Recombination

PubMed Central

Zhang, Qi; Li, Yuxue; Chen, Dandan; Yu, Yi; Duan, Lian; Shen, Ben; Liu, Wen

2010-01-01

The radical S-adenosylmethionine (S-AdoMet) superfamily contains thousands of proteins that catalyze highly diverse conversions, most of which are poorly understood due to a lack of information regarding chemical products and radical-dependent transformations. We here report that NosL, involved in forming the indole side ring of the thiopeptide nosiheptide (NOS), is a radical S-AdoMet 3-methyl-2-indolic acid (MIA) synthase. NosL catalyzed an unprecedented carbon chain reconstitution of L-Trp to give MIA, showing removal of the Cα-N unit and shift of the carboxylate to the indole ring. Dissection of the enzymatic process upon the identification of products and a putative glycyl intermediate uncovered a radical-mediated, unusual fragmentation-recombination reaction. This finding unveiled a key step in radical S-AdoMet enzyme-catalyzed structural rearrangements during complex biotransformations. Additionally, NosL tolerated fluorinated L-Trps as the substrates, allowing for production of a regiospecifically halogenated thiopeptide that has not been found in over 80 entity-containing, naturally occurring thiopeptide family. PMID:21240261

Electron transfer mediators accelerated the microbiologically influence corrosion against carbon steel by nitrate reducing Pseudomonas aeruginosa biofilm.

PubMed

Jia, Ru; Yang, Dongqing; Xu, Dake; Gu, Tingyue

2017-12-01

Electron transfer is a rate-limiting step in microbiologically influenced corrosion (MIC) caused by microbes that utilize extracellular electrons. Cross-cell wall electron transfer is necessary to transport the electrons released from extracellular iron oxidation into the cytoplasm of cells. Electron transfer mediators were found to accelerate the MIC caused by sulfate reducing bacteria. However, there is no publication in the literature showing the effect of electron transfer mediators on MIC caused by nitrate reducing bacteria (NRB). This work demonstrated that the corrosion of anaerobic Pseudomonas aeruginosa (PAO1) grown as a nitrate reducing bacterium biofilm on C1018 carbon steel was enhanced by two electron transfer mediators, riboflavin and flavin adenine dinucleotide (FAD) separately during a 7-day incubation period. The addition of either 10ppm (w/w) (26.6μM) riboflavin or 10ppm (12.7μM) FAD did not increase planktonic cell counts, but they increased the maximum pit depth on carbon steel coupons considerably from 17.5μm to 24.4μm and 25.0μm, respectively. Riboflavin and FAD also increased the specific weight loss of carbon steel from 2.06mg/cm 2 to 2.34mg/cm 2 and 2.61mg/cm 2 , respectively. Linear polarization resistance, electrochemical impedance spectroscopy and potentiodynamic polarization curves all corroborated the pitting and weight loss data. Copyright © 2017 Elsevier B.V. All rights reserved.

Absence of bacterial imprints on struvite-containing kidney stones: a structural investigation at the mesoscopic and atomic scale.

PubMed

Bazin, Dominique; André, Gilles; Weil, Raphael; Matzen, Guy; Emmanuel, Veron; Carpentier, Xavier; Daudon, M

2012-04-01

Bacterial imprints are always observed on highly carbonated apatite kidney stones but not struvite kidney stones. Struvite and carbonated apatite stones with a high CO(3)(2-)/PO(4)(3-) rate are believed to develop from infections, but their structural differences at the mesoscopic scale lack explanation. We investigated 17 urinary calculi composed mainly of struvite or carbonated apatite by Fourier transform infrared, scanning electron microscopy, and powder neutron diffraction techniques. Carbonated apatite but not struvite stones showed bacterial imprints. If the same stone contained both carbonated apatite and struvite components, bacterial imprints were observed on the carbonated apatite but not the struvite part. Moreover, neutron powder diffraction experiments revealed the crystal size of struvite stones were larger than that of carbonated apatite stones (250 ± 50 vs 50 nm). Bacterial imprints may appear more easily on kidney stones with small nanocrystals, such as carbonated apatite than with large nanocrystals, such as struvite. This approach may help identify bacteria contributing to stone formation, perhaps with negative results of urine culture. Copyright © 2012 Elsevier Inc. All rights reserved.

Bacterial community dynamics in a biodenitrification reactor packed with polylactic acid/poly (3-hydroxybutyrate-co-3-hydroxyvalerate) blend as the carbon source and biofilm carrier.

PubMed

Qiu, Tianlei; Xu, Ying; Gao, Min; Han, Meilin; Wang, Xuming

2017-05-01

While heterotrophic denitrification has been widely used for treating such nitrogen-rich wastewater, it requires the use of additional carbon sources. With fluctuations in the nitrate concentration in the influent, controlling the C/N ratio to avoid carbon breakthrough becomes difficult. To overcome this obstacle, solid-phase denitrification (SPD) using biodegradable polymers has been used, where denitrification and carbon source biodegradation depend on microorganisms growing within the reactor. However, the microbial community dynamics in continuous-flow SPD reactors have not been fully elucidated yet. Here, we aimed to study bacterial community dynamics in a biodenitrification reactor packed with a polylactic acid/poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PLA/PHBV) blend as the carbon source and biofilm carrier. A lab-scale denitrifying reactor filled with a PLA/PHBV blend was used. With 85 mg/L of influent NO 3 -N concentration and a hydraulic retention time (HRT) of 2.5 h, more than 92% of the nitrate was removed. The bacterial community of inoculated activated sludge had the highest species richness in all samples. Bacterial species diversity in the reactor first decreased and then increased to a stable level. Diaphorobacter species were predominant in the reactor after day 24. In total, 178 clones were retrieved from the 16S rRNA gene clone library constructed from the biofilm samples in the reactor at 62 days of operation, and 80.9% of the clones were affiliated with Betaproteobacteria. Of these, 97.2% were classified into phylotypes corresponding to Diaphorobacter nitroreducens strain NA10B with 99% sequence similarity. Diaphorobacter, Rhizobium, Acidovorax, Rubrivivax, Azospira, Thermomonas, and Acidaminobacter constituted the biofilm microflora in the stably running reactor. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Bacterial superantigens bypass Lck-dependent T cell receptor signaling by activating a Galpha11-dependent, PLC-beta-mediated pathway.

PubMed

Bueno, Clara; Lemke, Caitlin D; Criado, Gabriel; Baroja, Miren L; Ferguson, Stephen S G; Rahman, A K M Nur-Ur; Tsoukas, Constantine D; McCormick, John K; Madrenas, Joaquin

2006-07-01

The paradigm to explain antigen-dependent T cell receptor (TCR) signaling is based on the activation of the CD4 or CD8 coreceptor-associated kinase Lck. It is widely assumed that this paradigm is also applicable to signaling by bacterial superantigens. However, these bacterial toxins can activate human T cells lacking Lck, suggesting the existence of an additional pathway of TCR signaling. Here we showed that this alternative pathway operates in the absence of Lck-dependent tyrosine-phosphorylation events and was initiated by the TCR-dependent activation of raft-enriched heterotrimeric Galpha11 proteins. This event, in turn, activated a phospholipase C-beta and protein kinase C-mediated cascade that turned on the mitogen-activated protein kinases ERK-1 and ERK-2, triggered Ca(2+) influx, and translocated the transcription factors NF-AT and NF-kappaB to the nucleus, ultimately inducing the production of interleukin-2 in Lck-deficient T cells. The triggering of this alternative pathway by superantigens suggests that these toxins use a G protein-coupled receptor as a coreceptor on T cells.

Strontium Incorporation Into Calcite Generated by Bacterial Ureolysis

NASA Astrophysics Data System (ADS)

Fujita, Y.; Ingram, J. A.; Cortez, M. M.; Redden, G. D.; Smith, R. W.

2002-12-01

Strontium incorporation into calcite generated by bacterial ureolytic activity was investigated as part of a larger effort to evaluate the use of in situ urea hydrolysis for accelerating co-precipitation of trace metals and radionuclides in contaminated aquifers. 90Sr, a uranium fission product with a half-life of 29 years, is a significant subsurface contaminant at several Department of Energy facilities and could be immobilized using this remediation strategy. Experiments were conducted in a medium designed to simulate the groundwater of the Snake River Plain Aquifer in eastern Idaho, amended with strontium. Initially the solution was undersaturated with respect to calcite. As a model ureolytic organism, we used Bacillus pasteurii, a well-characterized bacterium known for high urease activity and previously shown to induce calcite precipitation in urea-amended medium. To gain information on the effect of the bacterial surfaces, we also looked at precipitation in the presence of a bacterial species that did not hydrolyze urea, as well as in the absence of bacteria. In the absence of bacterial ureolysis, carbonate precipitation was induced by addition of ammonium carbonate. All products were identified as calcite by X-ray diffraction. Strontium uptake was observed in all cases, but was greatest in the system including bacterial ureolysis. Sputter depth element profiling by time-of-flight secondary ion mass spectrometry (TOF-SIMS) confirmed this finding, showing highest Sr:Ca ratios in the bacterially generated calcite throughout the depth (~350 nm) investigated. Environmental Scanning Electron Microscopy (ESEM) of the solids revealed regular crystals containing the outlines of embedded or entombed bacterial cells, suggesting that calcite precipitated directly on the cell surfaces when present. Analysis by X-ray Absorption Near Edge Spectroscopy (XANES) indicated that in both the biotically and abiotically generated calcites the Sr was incorporated into the calcite

Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens.

PubMed

Higgins, Owen; Clancy, Eoin; Cormican, Martin; Boo, Teck Wee; Cunney, Robert; Smith, Terry J

2018-02-09

Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae , Neisseria meningitidis and Haemophilus influenzae . Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae , N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology.

Bioprecipitation of Calcium Carbonate Crystals by Bacteria Isolated from Saline Environments Grown in Culture Media Amended with Seawater and Real Brine

PubMed Central

Silva-Castro, G. A.; Uad, I.; Gonzalez-Martinez, A.; Rivadeneyra, A.; Gonzalez-Lopez, J.; Rivadeneyra, M. A.

2015-01-01

The precipitation of calcium carbonate and calcium sulphate by isolated bacteria from seawater and real brine obtained in a desalination plant growth in culture media containing seawater and brine as mineral sources has been studied. However, only bioprecipitation was detected when the bacteria were grown in media with added organic matter. Biomineralization process started rapidly, crystal formation taking place in the beginning a few days after inoculation of media; roughly 90% of total cultivated bacteria showed. Six major colonies with carbonate precipitation capacity dominated bacterial community structure cultivated in heterotrophic platable bacteria medium. Taxonomic identification of these six strains through partial 16S rRNA gene sequences showed their affiliation with Gram-positive Bacillus and Virgibacillus genera. These strains were able to form calcium carbonate minerals, which precipitated as calcite and aragonite crystals and showed bacterial fingerprints or bacteria calcification. Also, carbonic anhydrase activity was observed in three of these isolated bacteria. The results of this research suggest that microbiota isolated from sea water and brine is capable of precipitation of carbonate biominerals, which can occur in situ with mediation of organic matter concentrations. Moreover, calcium carbonate precipitation ability of this microbiota could be of importance in bioremediation of CO2 and calcium in certain environments. PMID:26273646

Bioprecipitation of Calcium Carbonate Crystals by Bacteria Isolated from Saline Environments Grown in Culture Media Amended with Seawater and Real Brine.

PubMed

Silva-Castro, G A; Uad, I; Gonzalez-Martinez, A; Rivadeneyra, A; Gonzalez-Lopez, J; Rivadeneyra, M A

2015-01-01

The precipitation of calcium carbonate and calcium sulphate by isolated bacteria from seawater and real brine obtained in a desalination plant growth in culture media containing seawater and brine as mineral sources has been studied. However, only bioprecipitation was detected when the bacteria were grown in media with added organic matter. Biomineralization process started rapidly, crystal formation taking place in the beginning a few days after inoculation of media; roughly 90% of total cultivated bacteria showed. Six major colonies with carbonate precipitation capacity dominated bacterial community structure cultivated in heterotrophic platable bacteria medium. Taxonomic identification of these six strains through partial 16S rRNA gene sequences showed their affiliation with Gram-positive Bacillus and Virgibacillus genera. These strains were able to form calcium carbonate minerals, which precipitated as calcite and aragonite crystals and showed bacterial fingerprints or bacteria calcification. Also, carbonic anhydrase activity was observed in three of these isolated bacteria. The results of this research suggest that microbiota isolated from sea water and brine is capable of precipitation of carbonate biominerals, which can occur in situ with mediation of organic matter concentrations. Moreover, calcium carbonate precipitation ability of this microbiota could be of importance in bioremediation of CO2 and calcium in certain environments.

Voltammetric Determination of Homocysteine Using Multiwall Carbon Nanotube Paste Electrode in the Presence of Chlorpromazine as a Mediator

PubMed Central

Gholami-Orimi, Fathali; Taleshi, Farshad; Biparva, Pourya; Karimi-Maleh, Hassan; Beitollahi, Hadi; Ebrahimi, Hamid R.; Shamshiri, Mohamad; Bagheri, Hasan; Fouladgar, Masoud; Taherkhani, Ali

2012-01-01

We propose chlorpromazine (CHP) as a new mediator for the rapid, sensitive, and highly selective voltammetric determination of homocysteine (Hcy) using multiwall carbon nanotube paste electrode (MWCNTPE). The experimental results showed that the carbon nanotube paste electrode has a highly electrocatalytic activity for the oxidation of Hcy in the presence of CHP as a mediator. Cyclic voltammetry, double potential step chronoamperometry, and square wave voltammetry (SWV) are used to investigate the suitability of CHP at the surface of MWCNTPE as a mediator for the electrocatalytic oxidation of Hcy in aqueous solutions. The kinetic parameters of the system, including electron transfer coefficient, and catalytic rate constant were also determined using the electrochemical approaches. In addition, SWV was used for quantitative analysis. SWV showed wide linear dynamic range (0.1–210.0 μM Hcy) with a detection limit of 0.08 μM Hcy. Finally, this method was also examined as a selective, simple, and precise electrochemical sensor for the determination of Hcy in real samples. PMID:22675657

A repeatedly refuelable mediated biofuel cell based on a hierarchical porous carbon electrode.

PubMed

Fujita, Shuji; Yamanoi, Shun; Murata, Kenichi; Mita, Hiroki; Samukawa, Tsunetoshi; Nakagawa, Takaaki; Sakai, Hideki; Tokita, Yuichi

2014-05-13

Biofuel cells that generate electricity from renewable fuels, such as carbohydrates, must be reusable through repeated refuelling, should these devices be used in consumer electronics. We demonstrate the stable generation of electricity from a glucose-powered mediated biofuel cell through multiple refuelling cycles. This refuelability is achieved by immobilizing nicotinamide adenine dinucleotide (NAD), an electron-transfer mediator, and redox enzymes in high concentrations on porous carbon particles constituting an anode while maintaining their electrochemical and enzymatic activities after the immobilization. This bioanode can be refuelled continuously for more than 60 cycles at 1.5 mA cm(-2) without significant potential drop. Cells assembled with these bioanodes and bilirubin-oxidase-based biocathodes can be repeatedly used to power a portable music player at 1 mW cm(-3) through 10 refuelling cycles. This study suggests that the refuelability within consumer electronics should facilitate the development of long and repeated use of the mediated biofuel cells as well as of NAD-based biosensors, bioreactors, and clinical applications.

A repeatedly refuelable mediated biofuel cell based on a hierarchical porous carbon electrode

PubMed Central

Fujita, Shuji; Yamanoi, Shun; Murata, Kenichi; Mita, Hiroki; Samukawa, Tsunetoshi; Nakagawa, Takaaki; Sakai, Hideki; Tokita, Yuichi

2014-01-01

Biofuel cells that generate electricity from renewable fuels, such as carbohydrates, must be reusable through repeated refuelling, should these devices be used in consumer electronics. We demonstrate the stable generation of electricity from a glucose-powered mediated biofuel cell through multiple refuelling cycles. This refuelability is achieved by immobilizing nicotinamide adenine dinucleotide (NAD), an electron-transfer mediator, and redox enzymes in high concentrations on porous carbon particles constituting an anode while maintaining their electrochemical and enzymatic activities after the immobilization. This bioanode can be refuelled continuously for more than 60 cycles at 1.5 mA cm−2 without significant potential drop. Cells assembled with these bioanodes and bilirubin-oxidase-based biocathodes can be repeatedly used to power a portable music player at 1 mW cm−3 through 10 refuelling cycles. This study suggests that the refuelability within consumer electronics should facilitate the development of long and repeated use of the mediated biofuel cells as well as of NAD-based biosensors, bioreactors, and clinical applications. PMID:24820210

In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cherrier, J.

Potential episodic hydrocarbon inputs associated with oil mining and transportation together with chronic introduction of hydrocarbons via urban runoff into the relatively pristine coastal Florida waters poses a significant threat to Florida's fragile marine environment. It is therefore important to understand the extent to which indigenous bacterial populations are able to degrade hydrocarbon compounds and also determine factors that could potentially control and promote the rate at which these compounds are broken down in situ. Previous controlled laboratory experiments carried out by our research group demonstrated that separately both photo-oxidation and cometabolism stimulate bacterial hydrocarbon degradation by natural bacterial assemblagesmore » collected from a chronically petroleum contaminated site in Bayboro Bay, Florida. Additionally, we also demonstrated that stable carbon and radiocarbon abundances of respired CO{sub 2} could be used to trace in situ hydrocarbon degradation by indigenous bacterial populations at this same site. This current proposal had two main objectives: (a) to evaluate the cumulative impact of cometabolism and photo-oxidation on hydrocarbon degradation by natural bacterial assemblages collected the same site in Bayboro Bay, Florida and (b) to determine if in situ hydrocarbon degradation by indigenous bacterial populations this site could be traced using natural radiocarbon and stable carbon abundances of assimilated bacterial carbon. Funds were used for 2 years of full support for one ESI Ph.D. student, April Croxton. To address our first objective a series of closed system bacterial incubations were carried out using photo-oxidized petroleum and pinfish (i.e. cometabolite). Bacterial production of CO{sub 2} was used as the indicator of hydrocarbon degradation and {delta}{sup 13}C analysis of the resultant CO{sub 2} was used to evaluate the source of the respired CO{sub 2} (i.e. petroleum hydrocarbons or the pinfish cometabolite

Mineralogical Controls on Carbon Cycling in a Floodplain Environment

NASA Astrophysics Data System (ADS)

Arora, B.; Dwivedi, D.; Steefel, C. I.; Spycher, N.; Fox, P. M.; Nico, P. S.

2016-12-01

With the overarching goal of understanding mineral-organic-microbe interactions on carbon and nutrient cycles, we are developing a reactive transport model that includes carbon (C) pools and transformations, a realistic treatment of protected C pools, multiple decomposition pathways, and radiocarbon (14C) dynamics. The objective of the modeling is to understand the impact of mineralogy on carbon turnover and residence times in a floodplain site in Rifle, CO. Previous studies have identified naturally reduced zones (NRZs) in the saturated zone of the Rifle site to be C hotspots and regions characterized by diffusion-limited transport and high rates of microbially-mediated biogeochemical reactions. Detailed characterization of the soil organic matter in both the NRZ and non-NRZ sediments at the Rifle site including radiocarbon dating, and extraction and chemical characterization of mineral-bound pool of organic matter, is used to inform the modeling. In this study, we describe the development of a coupled unsaturated-saturated flow and biogeochemical reactive transport model of the Rifle site along a two-dimensional cross-section (parallel to groundwater flow). The biogeochemical reaction network includes representations of bacterial and fungal activity, archetypal polymer and monomer carbon substrate groups, kinetic and equilibrium mineral precipitation and dissolution reactions, and aqueous and surface complexation. We use this model to explore fungal and bacterial community emergence at the site and compare organo-mineral interactions across NRZ and non-NRZ regions. Observed 14C profiles suggest that sediment-associated carbon in NRZ locations is much older than both the depositional age of the floodplain sediments and dissolved organic carbon in the groundwater. Model simulations were able to capture the observed soil organic matter (SOM) and Δ14C profiles across the Rifle site. Modeling results show higher lignin content in the NRZ sediments and greater Fe

Microalgal bacterial flocs treating paper mill effluent: A sunlight-based approach for removing carbon, nitrogen, phosphorus, and calcium.

PubMed

Van Den Hende, Sofie; Rodrigues, André; Hamaekers, Helen; Sonnenholzner, Stanislaus; Vervaeren, Han; Boon, Nico

2017-10-25

Treatment of upflow anaerobic sludge blanket (UASB) effluent from a paper mill in aerated activated sludge reactors involves high aeration costs. Moreover, this calcium-rich effluent leads to problematic scale formation. Therefore, a novel strategy for the aerobic treatment of paper mill UASB effluent in microalgal bacterial floc sequencing batch reactors (MaB-floc SBRs) is proposed, in which oxygen is provided via photosynthesis, and calcium is removed via bio-mineralization. Based on the results of batch experiments in the course of this study, a MaB-floc SBR was operated at an initial neutral pH. This SBR removed 58±21% organic carbon, 27±8% inorganic carbon, 77±5% nitrogen, 73±2% phosphorus, and 27±11% calcium. MaB-flocs contained 10±3% calcium, including biologically-influenced calcite crystals. The removal of calcium and inorganic carbon by MaB-flocs significantly decreased when inhibiting extracellular carbonic anhydrase (CA), an enzyme that catalyses the hydration and dehydration of CO 2 . This study demonstrates the potential of MaB-floc SBRs for the alternative treatment of calcium-rich paper mill effluent, and highlights the importance of extracellular CA in this treatment process. Copyright © 2017 Elsevier B.V. All rights reserved.

Altered Functionality of Anti-Bacterial Antibodies in Patients with Chronic Hepatitis C Virus Infection

PubMed Central

Lamontagne, Anne; Long, Ronald E.; Comunale, Mary Ann; Hafner, Julie; Rodemich-Betesh, Lucy; Wang, Mengjun; Marrero, Jorge; Di Bisceglie, Adrian M.; Block, Timothy; Mehta, Anand

2013-01-01

Background Using comparative glycoproteomics, we have previously identified a glycoprotein that is altered in both amount and glycosylation as a function of liver cirrhosis. The altered glycoprotein is an agalactosylated (G0) immunoglobulin G molecule (IgG) that recognizes the heterophilic alpha-gal epitope. Since the alpha gal epitope is found on gut enterobacteria, it has been hypothesized that anti-gal antibodies are generated as a result of increased bacterial exposure in patients with liver disease. Methods The N-linked glycosylation of anti-gal IgG molecules from patients with fibrosis and cirrhosis was determined and the effector function of anti-bacterial antibodies from over 100 patients examined. In addition, markers of microbial exposure were determined. Results Surprisingly, the subset of agalactosylated anti-gal antibodies described here, was impaired in their ability to mediate complement mediated lysis and inhibited the complement-mediated destruction of common gut bacteria. In an analysis of serum from more than 100 patients with liver disease, we have shown that those with increased levels of this modified anti-gal antibody had increased levels of markers of bacterial exposure. Conclusions Anti-gal antibodies in patients with liver cirrhosis were reduced in their ability to mediate complement mediated lysis of target cells. As bacterial infection is a major complication in patients with cirrhosis and bacterial products such as LPS are thought to play a major role in the development and progression of liver fibrosis, this finding has many clinical implications in the etiology, prognosis and treatment of liver disease. PMID:23750224

Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development.

PubMed

Engineer, Cawas B; Ghassemian, Majid; Anderson, Jeffrey C; Peck, Scott C; Hu, Honghong; Schroeder, Julian I

2014-09-11

Environmental stimuli, including elevated carbon dioxide levels, regulate stomatal development; however, the key mechanisms mediating the perception and relay of the CO2 signal to the stomatal development machinery remain elusive. To adapt CO2 intake to water loss, plants regulate the development of stomatal gas exchange pores in the aerial epidermis. A diverse range of plant species show a decrease in stomatal density in response to the continuing rise in atmospheric CO2 (ref. 4). To date, one mutant that exhibits deregulation of this CO2-controlled stomatal development response, hic (which is defective in cell-wall wax biosynthesis, ref. 5), has been identified. Here we show that recently isolated Arabidopsis thaliana β-carbonic anhydrase double mutants (ca1 ca4) exhibit an inversion in their response to elevated CO2, showing increased stomatal development at elevated CO2 levels. We characterized the mechanisms mediating this response and identified an extracellular signalling pathway involved in the regulation of CO2-controlled stomatal development by carbonic anhydrases. RNA-seq analyses of transcripts show that the extracellular pro-peptide-encoding gene EPIDERMAL PATTERNING FACTOR 2 (EPF2), but not EPF1 (ref. 9), is induced in wild-type leaves but not in ca1 ca4 mutant leaves at elevated CO2 levels. Moreover, EPF2 is essential for CO2 control of stomatal development. Using cell-wall proteomic analyses and CO2-dependent transcriptomic analyses, we identified a novel CO2-induced extracellular protease, CRSP (CO2 RESPONSE SECRETED PROTEASE), as a mediator of CO2-controlled stomatal development. Our results identify mechanisms and genes that function in the repression of stomatal development in leaves during atmospheric CO2 elevation, including the carbonic-anhydrase-encoding genes CA1 and CA4 and the secreted protease CRSP, which cleaves the pro-peptide EPF2, in turn repressing stomatal development. Elucidation of these mechanisms advances the understanding

Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development

PubMed Central

Engineer, Cawas B.; Ghassemian, Majid; Anderson, Jeffrey C.; Peck, Scott C.; Hu, Honghong; Schroeder, Julian I.

2014-01-01

Environmental stimuli, including elevated carbon dioxide levels, regulate stomatal development1–3; however, the key mechanisms mediating the perception and relay of the CO2 signal to the stomatal development machinery remain elusive. To adapt CO2 intake to water loss, plants regulate the development of stomatal gas exchange pores in the aerial epidermis. A diverse range of plant species show a decrease in stomatal density in response to the continuing rise in atmospheric CO2 (ref. 4). To date, one mutant that exhibits deregulation of this CO2-controlled stomatal development response, hic (which is defective in cell-wall wax biosynthesis, ref. 5), has been identified. Here we show that recently isolated Arabidopsis thaliana β-carbonic anhydrase double mutants (ca1 ca4)6 exhibit aninversion in their response to elevated CO2, showing increased stomatal development at elevated CO2 levels. We characterized the mechanisms mediating this response and identified an extracellular signalling pathway involved in the regulation of CO2-controlled stomatal development by carbonic anhydrases. RNA-seq analyses of transcripts show that the extracellular pro-peptide-encoding gene EPIDERMAL PATTERNING FACTOR 2 (EPF2)7,8, but not EPF1 (ref. 9), is induced in wild-type leaves but not inca1 ca4 mutant leaves at elevated CO2 levels. Moreover, EPF2 is essential for CO2 control of stomatal development. Using cell-wall proteomic analyses and CO2-dependent transcriptomic analyses, we identified a novel CO2-induced extracellular protease, CRSP (CO2 RESPONSE SECRETED PROTEASE), as a mediator of CO2-controlled stomatal development. Our results identify mechanisms and genes that function in the repression of stomatal development in leaves during atmospheric CO2 elevation, including the carbonic-anhydrase-encoding genes CA1 and CA4 and the secreted protease CRSP, which cleaves the pro-peptide EPF2, in turn repressing stomatal development. Elucidation of these mechanisms advances the

Marine mesocosm bacterial colonisation of volcanic ash

NASA Astrophysics Data System (ADS)

Witt, Verena; Cimarelli, Corrado; Ayris, Paul; Kueppers, Ulrich; Erpenbeck, Dirk; Dingwell, Donald; Woerheide, Gert

2015-04-01

Volcanic eruptions regularly eject large quantities of ash particles into the atmosphere, which can be deposited via fallout into oceanic environments. Such fallout has the potential to alter pH, light and nutrient availability at local scales. Shallow-water coral reef ecosystems - "rainforests of the sea" - are highly sensitive to disturbances, such as ocean acidification, sedimentation and eutrophication. Therefore, wind-delivered volcanic ash may lead to burial and mortality of such reefs. Coral reef ecosystem resilience may depend on pioneer bacterial colonisation of the ash layer, supporting subsequent establishment of the micro- and ultimately the macro-community. However, which bacteria are involved in pioneer colonisation remain unknown. We hypothesize that physico-chemical properties (i.e., morphology, mineralogy) of the ash may dictate bacterial colonisation. The effect of substrate properties on bacterial colonisation was tested by exposing five substrates: i) quartz sand ii) crystalline ash (Sakurajima, Japan) iii) volcanic glass iv) carbonate reef sand and v) calcite sand of similar grain size, in controlled marine coral reef aquaria under low light conditions for six months. Bacterial communities were screened every month by Automated Ribosomal Intergenic Spacer Analysis of the 16S-23S rRNA Internal Transcribed Spacer region. Multivariate statistics revealed discrete groupings of bacterial communities on substrates of volcanic origin (ash and glass) and reef origin (three sands). Analysis of Similarity supported significantly different communities associated with all substrates (p=0.0001), only quartz did not differ from both carbonate and calcite sands. The ash substrate exhibited the most diverse bacterial community with the most substrate-specific bacterial operational taxonomic units. Our findings suggest that bacterial diversity and community composition during colonisation of volcanic ash in a coral reef-like environment is controlled by the

Marine Mesocosm Bacterial Colonisation of Volcanic Ash

NASA Astrophysics Data System (ADS)

Witt, V.; Cimarelli, C.; Ayris, P. M.; Kueppers, U.; Erpenbeck, D.; Dingwell, D. B.; Woerheide, G.

2014-12-01

Explosive volcanic eruptions regularly eject large quantities of ash particles into the atmosphere, which can be deposited via fallout into oceanic environments. Such fallout has the potential to alter pH, light and nutrient availability at local or regional scales. Shallow-water coral reef ecosystems - "rainforests of the sea" - are highly sensitive to disturbances, such as ocean acidification, sedimentation and eutrophication. Therefore, ash deposition may lead to burial and mortality of such reefs. Coral reef ecosystem resilience may depend on pioneer bacterial colonisation of the ash layer, supporting subsequent establishment of the micro- and ultimately the macro-community. However, it is currently unknown which bacteria are involved in pioneer colonisation. We hypothesize that physico-chemical properties (i.e., morphology, chemistry, mineralogy) of the ash may dictate bacterial colonisation. We have tested the effect of substrate properties on bacterial diversity and abundance colonising five substrates: i) quartz sand ii) crystalline ash from the Sakurajima volcano (Japan) iii) volcanic glass iv) carbonate reef sand and v) calcite sand of similar grain size - by incubation in a controlled marine mesocosm (coral reef aquarium) under low light conditions for three months. Bacterial communities were screened every month by Automated Ribosomal Intergenic Spacer Analysis of the 16S-23S rRNA Internal Transcribed Spacer region. Multivariate statistics revealed discrete groupings of bacterial communities on substrates of volcanic origin (ash and glass) and reef origin (three sands). Analysis Of Similarity supports significantly different communities associated with all substrates (p=0.0001), only quartz did not differ from both carbonate and calcite sands. The ash substrate exhibited the most diverse bacterial community and carried the most substrate-specific bacterial operational taxonomic units. Our findings suggest that bacterial diversity and community

A Common Fold Mediates Vertebrate Defense and Bacterial Attack

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosado, Carlos J.; Buckle, Ashley M.; Law, Ruby H.P.

2008-10-02

Proteins containing membrane attack complex/perforin (MACPF) domains play important roles in vertebrate immunity, embryonic development, and neural-cell migration. In vertebrates, the ninth component of complement and perforin form oligomeric pores that lyse bacteria and kill virus-infected cells, respectively. However, the mechanism of MACPF function is unknown. We determined the crystal structure of a bacterial MACPF protein, Plu-MACPF from Photorhabdus luminescens, to 2.0 angstrom resolution. The MACPF domain reveals structural similarity with poreforming cholesterol-dependent cytolysins (CDCs) from Gram-positive bacteria. This suggests that lytic MACPF proteins may use a CDC-like mechanism to form pores and disrupt cell membranes. Sequence similarity between bacterialmore » and vertebrate MACPF domains suggests that the fold of the CDCs, a family of proteins important for bacterial pathogenesis, is probably used by vertebrates for defense against infection.« less

Bisphenols: Application, occurrence, safety, and biodegradation mediated by bacterial communities in wastewater treatment plants and rivers.

PubMed

Noszczyńska, Magdalena; Piotrowska-Seget, Zofia

2018-06-01

Numerous data indicate that most of bisphenols (BPs) are endocrine disrupters and exhibit cytotoxicity, neurotoxicity, genotoxicity and reproductive toxicity against vertebrates. Nevertheless, they are widely applied in material production what result in their ubiquitous occurrence in ecosystems. While BPA is the most frequently detected in environment, BPAF, BPF and BPS are also often found. Ecosystem particularly exposed to BPs pollution is industrial and municipal wastewater being a common source of BPA in river waters. Different techniques to remove BPs from these ecosystems have been applied, among which biodegradation seems to be the most effective. In this review the current state of knowledge in the field of BPs application, distribution in the environment, effects on animal and human health, and biodegradation mediated by bacterial populations in wastewater treatment plants and rivers is presented. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bacterial vaginosis and preterm birth.

PubMed

Manns-James, Laura

2011-01-01

Although it has been clear for more than 2 decades that bacterial vaginosis increases the risk for preterm birth in some women, it is not yet fully understood why this association exists or how best to modify the risk. Incomplete understanding of this polymicrobial condition and difficulties in classification contribute to the challenge. The relationship between altered vaginal microflora and preterm birth is likely mediated by host immune responses. Because treatment of bacterial vaginosis during pregnancy does not improve preterm birth rates, and may in fact increase them, screening and treatment of asymptomatic pregnant women is discouraged. Symptomatic women should be treated for symptom relief. This article reviews the pathophysiology of bacterial vaginosis and controversy surrounding management during pregnancy. Agents currently recommended for treatment of this condition are reviewed. © 2011 by the American College of Nurse-Midwives.

Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

NASA Astrophysics Data System (ADS)

Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

2011-12-01

The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum

Spatiotemporal drivers of dissolved organic matter in high alpine lakes: Role of Saharan dust inputs and bacterial activity.

PubMed

Mladenov, Natalie; Pulido-Villena, Elvira; Morales-Baquero, Rafael; Ortega-Retuerta, Eva; Sommaruga, Ruben; Reche, Isabel

2008-01-01

The effects of many environmental stressors such as UV radiation are mediated by dissolved organic matter (DOM) properties. Therefore, determining the factors shaping spatial and temporal patterns is particularly essential in the most susceptible, low dissolved organic carbon (DOC) lakes. We analyzed spatiotemporal variations in dissolved organic carbon concentration and dissolved organic matter optical properties (absorption and fluorescence) in 11 transparent lakes located above tree line in the Sierra Nevada Mountains (Spain), and we assessed potential external (evaporation and atmospheric deposition) and internal (bacterial abundance, bacterial production, chlorophyll a, and catchment vegetation) drivers of DOM patterns. At spatial and temporal scales, bacteria were related to chromophoric DOM (CDOM). At the temporal scale, water soluble organic carbon (WSOC) in dust deposition and evaporation were found to have a significant influence on DOC and CDOM in two Sierra Nevada lakes studied during the ice-free periods of 2000-2002. DOC concentrations and absorption coefficients at 320 nm were strongly correlated over the spatial scale (n = 11, R(2) = 0.86; p < 0.01), but inconsistently correlated over time, indicating seasonal and interannual variability in external factors and a differential response of DOC concentration and CDOM to these factors. At the continental scale, higher mean DOC concentrations and more CDOM in lakes of the Sierra Nevada than in lakes of the Pyrenees and Alps may be due to a combination of more extreme evaporation, and greater atmospheric dust deposition.

Spatiotemporal drivers of dissolved organic matter in high alpine lakes: Role of Saharan dust inputs and bacterial activity

PubMed Central

Mladenov, Natalie; Pulido-Villena, Elvira; Morales-Baquero, Rafael; Ortega-Retuerta, Eva; Sommaruga, Ruben; Reche, Isabel

2010-01-01

The effects of many environmental stressors such as UV radiation are mediated by dissolved organic matter (DOM) properties. Therefore, determining the factors shaping spatial and temporal patterns is particularly essential in the most susceptible, low dissolved organic carbon (DOC) lakes. We analyzed spatiotemporal variations in dissolved organic carbon concentration and dissolved organic matter optical properties (absorption and fluorescence) in 11 transparent lakes located above tree line in the Sierra Nevada Mountains (Spain), and we assessed potential external (evaporation and atmospheric deposition) and internal (bacterial abundance, bacterial production, chlorophyll a, and catchment vegetation) drivers of DOM patterns. At spatial and temporal scales, bacteria were related to chromophoric DOM (CDOM). At the temporal scale, water soluble organic carbon (WSOC) in dust deposition and evaporation were found to have a significant influence on DOC and CDOM in two Sierra Nevada lakes studied during the ice-free periods of 2000–2002. DOC concentrations and absorption coefficients at 320 nm were strongly correlated over the spatial scale (n = 11, R2 = 0.86; p < 0.01), but inconsistently correlated over time, indicating seasonal and interannual variability in external factors and a differential response of DOC concentration and CDOM to these factors. At the continental scale, higher mean DOC concentrations and more CDOM in lakes of the Sierra Nevada than in lakes of the Pyrenees and Alps may be due to a combination of more extreme evaporation, and greater atmospheric dust deposition. PMID:20582227

Curcumin Quantum Dots Mediated Degradation of Bacterial Biofilms.

PubMed

Singh, Ashish K; Prakash, Pradyot; Singh, Ranjana; Nandy, Nabarun; Firdaus, Zeba; Bansal, Monika; Singh, Ranjan K; Srivastava, Anchal; Roy, Jagat K; Mishra, Brahmeshwar; Singh, Rakesh K

2017-01-01

Bacterial biofilm has been reported to be associated with more than 80% of bacterial infections. Curcumin, a hydrophobic polyphenol compound, has anti-quorum sensing activity apart from having antimicrobial action. However, its use is limited by its poor aqueous solubility and rapid degradation. In this study, we attempted to prepare quantum dots of the drug curcumin in order to achieve enhanced solubility and stability and investigated for its antimicrobial and antibiofilm activity. We utilized a newer two-step bottom up wet milling approach to prepare Curcumin Quantum Dots (CurQDs) using acetone as a primary solvent. Minimum inhibitory concentration against select Gram-positive and Gram-negative bacteria was performed. The antibiofilm assay was performed at first using 96-well tissue culture plate and subsequently validated by Confocal Laser Scanning Microscopy. Further, biofilm matrix protein was isolated using formaldehyde sludge and TCA/Acetone precipitation method. Protein extracted was incubated with varying concentration of CurQDs for 4 h and was subjected to SDS-PAGE. Molecular docking study was performed to observe interaction between curcumin and phenol soluble modulins as well as curli proteins. The biophysical evidences obtained from TEM, SEM, UV-VIS, fluorescence, Raman spectroscopy, and zeta potential analysis confirmed the formation of curcumin quantum dots with increased stability and solubility. The MICs of curcumin quantum dots, as observed against both select gram positive and negative bacterial isolates, was observed to be significantly lower than native curcumin particles. On TCP assay, Curcumin observed to be having antibiofilm as well as biofilm degrading activity. Results of SDS-PAGE and molecular docking have shown interaction between biofilm matrix proteins and curcumin. The results indicate that aqueous solubility and stability of Curcumin can be achieved by preparing its quantum dots. The study also demonstrates that by sizing down the

β-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity

PubMed Central

Gutierrez, A.; Laureti, L.; Crussard, S.; Abida, H.; Rodríguez-Rojas, A.; Blázquez, J.; Baharoglu, Z.; Mazel, D.; Darfeuille, F.; Vogel, J.; Matic, I.

2013-01-01

Regardless of their targets and modes of action, subinhibitory concentrations of antibiotics can have an impact on cell physiology and trigger a large variety of cellular responses in different bacterial species. Subinhibitory concentrations of β-lactam antibiotics cause reactive oxygen species production and induce PolIV-dependent mutagenesis in Escherichia coli. Here we show that subinhibitory concentrations of β-lactam antibiotics induce the RpoS regulon. RpoS-regulon induction is required for PolIV-dependent mutagenesis because it diminishes the control of DNA-replication fidelity by depleting MutS in E. coli, Vibrio cholerae and Pseudomonas aeruginosa. We also show that in E. coli, the reduction in mismatch-repair activity is mediated by SdsR, the RpoS-controlled small RNA. In summary, we show that mutagenesis induced by subinhibitory concentrations of antibiotics is a genetically controlled process. Because this mutagenesis can generate mutations conferring antibiotic resistance, it should be taken into consideration for the development of more efficient antimicrobial therapeutic strategies. PMID:23511474

Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens

PubMed Central

Clancy, Eoin; Cormican, Martin; Boo, Teck Wee; Cunney, Robert

2018-01-01

Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae. Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae, N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology. PMID:29425124

Bacterial nucleotide-based second messengers.

PubMed

Pesavento, Christina; Hengge, Regine

2009-04-01

In all domains of life nucleotide-based second messengers transduce signals originating from changes in the environment or in intracellular conditions into appropriate cellular responses. In prokaryotes cyclic di-GMP has emerged as an important and ubiquitous second messenger regulating bacterial life-style transitions relevant for biofilm formation, virulence, and many other bacterial functions. This review describes similarities and differences in the architecture of the cAMP, (p)ppGpp, and c-di-GMP signaling systems and their underlying signaling principles. Moreover, recent advances in c-di-GMP-mediated signaling will be presented and the integration of c-di-GMP signaling with other nucleotide-based signaling systems will be discussed.

Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats.

PubMed

Han, Pu; Deem, Michael W

2017-02-01

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR. When bacteria have a small rate of deleting spacers, a new parameter region in which bacteria and viruses can coexist arises, and it leads to a more complex coexistence patten for bacteria and viruses. For example, when the virus mutation rate is low, the virus extinction probability changes non-montonically with the bacterial exposure rate. The virus and bacteria coevolution not only alters the virus extinction probability, but also changes the bacterial population structure. Additionally, we show that recombination is a successful strategy for viruses to escape from CRISPR recognition when viruses have multiple proto-spacers, providing support for a recombination-mediated escape mechanism suggested experimentally. Finally, we suggest that the re-entrant phase diagram, in which phages can progress through three phases of extinction and two phases of abundance at low spacer deletion rates as a function of exposure rate to bacteria, is an experimentally testable phenomenon. © 2017 The Author(s).

Sterilization of bacterial spores by using supercritical carbon dioxide and hydrogen peroxide.

PubMed

Hemmer, Jason D; Drews, Michael J; LaBerge, Martine; Matthews, Michael A

2007-02-01

It was hypothesized that supercritical carbon dioxide (SC-CO(2)) treatment could serve as an alternative sterilization method at various temperatures (40-105 degrees C), CO(2) pressures (200-680 atm), and treatment times (25 min to 6 h), and with or without the use of a passive additive (distilled water, dH(2)O) or an active additive (hydrogen peroxide, H(2)O(2)). While previous researchers have shown that SC-CO(2) possesses antimicrobial properties, sterilization effectiveness has not been shown at sufficiently low treatment temperatures and cycle times, using resistant bacterial spores. Experiments were conducted using Geobacillus stearothermophilus and Bacillus atrophaeus spores. Spore strips were exposed to SC-CO(2) in commercially available supercritical fluid extraction and reaction systems, at varying temperatures, pressures, treatment times, and with or without the use of a passive additive, such as dH(2)O, or an active additive, such as H(2)O(2). Treatment parameters were varied from 40 to 105 degrees C, 200-680 atm, and from 25 min to 6 h. At 105 degrees C without H(2)O(2), both spore types were completely deactivated at 300 atm in 25 min, a shorter treatment cycle than is obtained with methods in use today. On the other hand, with added H(2)O(2) (<100 ppm), 6 log populations of both spore types were completely deactivated using SC-CO(2) in 1 h at 40 degrees C. It was concluded from the data that large populations of resistant bacterial spores can be deactivated with SC-CO(2) with added H(2)O(2)at lower temperatures and potentially shorter treatment cycles than in most sterilization methods in use today. (c) 2006 Wiley Periodicals, Inc.

Root bacterial endophytes alter plant phenotype, but not physiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henning, Jeremiah A.; Weston, David J.; Pelletier, Dale A.

Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. Here, we chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, netmore » photosynthesis, net photosynthesis at saturating light–A sat, and saturating CO 2–A max). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.« less

Root bacterial endophytes alter plant phenotype, but not physiology

DOE PAGES

Henning, Jeremiah A.; Weston, David J.; Pelletier, Dale A.; ...

2016-11-01

Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. Here, we chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, netmore » photosynthesis, net photosynthesis at saturating light–A sat, and saturating CO 2–A max). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.« less

Increased resiliency and activity of microbial mediated carbon cycling enzymes in diversified bioenergy cropping systems

NASA Astrophysics Data System (ADS)

Upton, R.; Bach, E.; Hofmockel, K. S.

2017-12-01

Microbes are mediators of soil carbon (C) and are influenced in membership and activity by nitrogen (N) fertilization and inter-annual abiotic factors. Microbial communities and their extracellular enzyme activities (EEA) are important parameters that influence ecosystem C cycling properties and are often included in microbial explicit C cycling models. In an effort to generate model relevant, empirical findings, we investigated how both microbial community structure and C degrading enzyme activity are influenced by inter-annual variability and N inputs in bioenergy crops. Our study was performed at the Comparison of Biofuel Systems field-site from 2011 to 2014, in three bioenergy cropping systems, continuous corn (CC) and two restored prairies, both fertilized (FP) and unfertilized (P). We hypothesized microbial community structure would diverge during the prairie restoration, leading to changes in C cycling enzymes over time. Using a sequencing approach (16S and ITS) we determined the bacterial and fungal community structure response to the cropping system, fertilization, and inter-annual variability. Additionally, we used EEA of β-glucosidase, cellobiohydrolase, and β-xylosidase to determine inter-annual and ecosystem impacts on microbial activity. Our results show cropping system was a main effect for microbial community structure, with corn diverging from both prairies to be less diverse. Inter-annual changes showed that a drought occurring in 2012 significantly impacted microbial community structure in both the P and CC, decreasing microbial richness. However, FP increased in microbial richness, suggesting the application of N increased resiliency to drought. Similarly, the only year in which C cycling enzymes were impacted by ecosystem was 2012, with FP supporting higher potential enzymatic activity then CC and P. The highest EEA across all ecosystems occurred in 2014, suggesting the continued root biomass and litter build-up in this no till system

Agrobacterium tumefaciens-mediated transformation of oleaginous yeast Lipomyces species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, Ziyu; Deng, Shuang; Culley, David E.

Background: Because of interest in the production of renewable bio-hydrocarbon fuels, various living organisms have been explored for their potential use in producing fuels and chemicals. The oil-producing (oleaginous) yeast Lipomyces starkeyi is the subject of active research regarding the production of lipids using a wide variety of carbon and nutrient sources. The genome of L. starkeyi has been published, which opens the door to production strain improvements using the tools of synthetic biology and metabolic engineering. However, using these tools for strain improvement requires the establishment of effective and reliable transformation methods with suitable selectable markers (antibiotic resistance ormore » auxotrophic marker genes) and the necessary genetic elements (promoters and terminators) for expression of introduced genes. Chemical-based methods have been published, but suffer from low efficiency or the requirement for targeting to rRNA loci. To address these problems, Agrobacterium-mediated transformation was investigated as an alternative method for L. starkeyi and other Lipomyces species. Results: In this study, Agrobacterium-mediated transformation was demonstrated to be effective in the transformation of both L. starkeyi and other Lipomyces species and that the introduced DNA can be reliably integrated into the chromosomes of these species. The gene deletion of Ku70 and Pex10 was also demonstrated in L. starkeyi. In addition to the bacterial antibiotic selection marker gene hygromycin B phosphotransferase, the bacterial -glucuronidase reporter gene under the control of L. starkeyi translation elongation factor 1 promoter was also stably expressed in seven different Lipomyces species. Conclusion: The results from this study clearly demonstrate that Agrobacterium-mediated transformation is a reliable genetic tool for gene deletion and integration and expression of heterologous genes in L. starkeyi and other Lipomyces species.« less

Agrobacterium tumefaciens-mediated transformation of oleaginous yeast Lipomyces species.

PubMed

Dai, Ziyu; Deng, Shuang; Culley, David E; Bruno, Kenneth S; Magnuson, Jon K

2017-08-01

Interest in using renewable sources of carbon, especially lignocellulosic biomass, for the production of hydrocarbon fuels and chemicals has fueled interest in exploring various organisms capable of producing hydrocarbon biofuels and chemicals or their precursors. The oleaginous (oil-producing) yeast Lipomyces starkeyi is the subject of active research regarding the production of triacylglycerides as hydrocarbon fuel precursors using a variety of carbohydrate and nutrient sources. The genome of L. starkeyi has been published, which opens the door to production strain improvements through the development and use of the tools of synthetic biology for this oleaginous species. The first step in establishment of synthetic biology tools for an organism is the development of effective and reliable transformation methods with suitable selectable marker genes and demonstration of the utility of the genetic elements needed for expression of introduced genes or deletion of endogenous genes. Chemical-based methods of transformation have been published but suffer from low efficiency. To address these problems, Agrobacterium-mediated transformation was investigated as an alternative method for L. starkeyi and other Lipomyces species. In this study, Agrobacterium-mediated transformation was demonstrated to be effective in the transformation of both L. starkeyi and other Lipomyces species. The deletion of the peroxisomal biogenesis factor 10 gene was also demonstrated in L. starkeyi. In addition to the bacterial antibiotic selection marker gene hygromycin B phosphotransferase, the bacterial β-glucuronidase reporter gene under the control of L. starkeyi translation elongation factor 1α promoter was also stably expressed in six different Lipomyces species. The results from this study demonstrate that Agrobacterium-mediated transformation is a reliable and effective genetic tool for homologous recombination and expression of heterologous genes in L. starkeyi and other Lipomyces

Fungal–bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality

PubMed Central

Fabian, Jenny; Zlatanovic, Sanja; Mutz, Michael; Premke, Katrin

2017-01-01

Ecological functions of fungal and bacterial decomposers vary with environmental conditions. However, the response of these decomposers to particulate organic matter (POM) quality, which varies widely in aquatic ecosystems, remains poorly understood. Here we investigated how POM pools of substrates of different qualities determine the relative contributions of aquatic fungi and bacteria to terrigenous carbon (C) turnover. To this end, surface sediments were incubated with different POM pools of algae and/or leaf litter. 13C stable-isotope measurements of C mineralization were combined with phospholipid analysis to link the metabolic activities and substrate preferences of fungal and bacterial heterotrophs to dynamics in their abundance. We found that the presence of labile POM greatly affected the dominance of bacteria over fungi within the degrader communities and stimulated the decomposition of beech litter primarily through an increase in metabolic activity. Our data indicated that fungi primarily contribute to terrigenous C turnover by providing litter C for the microbial loop, whereas bacteria determine whether the supplied C substrate is assimilated into biomass or recycled back into the atmosphere in relation to phosphate availability. Thus, this study provides a better understanding of the role of fungi and bacteria in terrestrial–aquatic C cycling in relation to environmental conditions. PMID:27983721

Bacterial and cellular RNAs at work during Listeria infection.

PubMed

Sesto, Nina; Koutero, Mikael; Cossart, Pascale

2014-01-01

Listeria monocytogenes is an intracellular pathogen that can enter and invade host cells. In the course of its infection, RNA-mediated regulatory mechanisms provide a fast and versatile response for both the bacterium and the host. They regulate a variety of processes, such as environment sensing and virulence in pathogenic bacteria, as well as development, cellular differentiation, metabolism and immune responses in eukaryotic cells. The aim of this article is to summarize first the RNA-mediated regulatory mechanisms that play a role in the Listeria lifestyle and in its virulence, and then the host miRNA responses to Listeria infection. Finally, we discuss the potential cross-talk between bacterial RNAs and host RNA regulatory mechanisms as new mechanisms of bacterial virulence.

Bacterial-cellulose-derived interconnected meso-microporous carbon nanofiber networks as binder-free electrodes for high-performance supercapacitors

NASA Astrophysics Data System (ADS)

Hao, Xiaodong; Wang, Jie; Ding, Bing; Wang, Ya; Chang, Zhi; Dou, Hui; Zhang, Xiaogang

2017-06-01

Bacterial cellulose (BC), a typical biomass prepared from the microbial fermentation process, has been proved that it can be an ideal platform for design of three-dimensional (3D) multifunctional nanomaterials in energy storage and conversion field. Here we developed a simple and general silica-assisted strategy for fabrication of interconnected 3D meso-microporous carbon nanofiber networks by confine nanospace pyrolysis of sustainable BC, which can be used as binder-free electrodes for high-performance supercapacitors. The synthesized carbon nanofibers exhibited the features of interconnected 3D networks architecture, large surface area (624 m2 g-1), mesopores-dominated hierarchical porosity, and high graphitization degree. The as-prepared electrode (CN-BC) displayed a maximum specific capacitance of 302 F g-1 at a current density of 0.5 A g-1, high-rate capability and good cyclicity in 6 M KOH electrolyte. This work, together with cost-effective preparation strategy to make high-value utilization of cheap biomass, should have significant implications in the green and mass-producible energy storage.

Herbivore-mediated material fluxes in a northern deciduous forest under elevated carbon dioxide and ozone concentrations.

PubMed

Meehan, Timothy D; Couture, John J; Bennett, Alison E; Lindroth, Richard L

2014-10-01

Anthropogenic changes in atmospheric carbon dioxide (CO2 ) and ozone (O3 ) are known to alter tree physiology and growth, but the cascading effects on herbivore communities and herbivore-mediated nutrient cycling are poorly understood. We sampled herbivore frass, herbivore-mediated greenfall, and leaf-litter deposition in temperate forest stands under elevated CO2 (c. 560 ppm) and O3 (c. 1.5× ambient), analyzed substrate chemical composition, and compared the quality and quantity of fluxes under multiple atmospheric treatments. Leaf-chewing herbivores fluxed 6.2 g m(-2)  yr(-1) of frass and greenfall from the canopy to the forest floor, with a carbon : nitrogen (C : N) ratio 32% lower than that of leaf litter. Herbivore fluxes of dry matter, C, condensed tannins, and N increased under elevated CO2 (35, 32, 63 and 39%, respectively), while fluxes of N decreased (18%) under elevated O3 . Herbivore-mediated dry matter inputs scaled across atmospheric treatments as a constant proportion of leaf-litter inputs. Increased fluxes under elevated CO2 were consistent with increased herbivore consumption and abundance, and with increased plant growth and soil respiration, previously reported for this experimental site. Results suggest that insect herbivory will reinforce other factors, such as photosynthetic rate and fine-root production, impacting C sequestration by forests in future environments. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

Unravelling the Carbon and Sulphur Metabolism in Coastal Soil Ecosystems Using Comparative Cultivation-Independent Genome-Level Characterisation of Microbial Communities

PubMed Central

Yousuf, Basit; Kumar, Raghawendra; Mishra, Avinash; Jha, Bhavanath

2014-01-01

Bacterial autotrophy contributes significantly to the overall carbon balance, which stabilises atmospheric CO2 concentration and decelerates global warming. Little attention has been paid to different modes of carbon/sulphur metabolism mediated by autotrophic bacterial communities in terrestrial soil ecosystems. We studied these pathways by analysing the distribution and abundance of the diagnostic metabolic marker genes cbbM, apsA and soxB, which encode for ribulose-1,5-bisphosphate carboxylase/oxygenase, adenosine phosphosulphate reductase and sulphate thiohydrolase, respectively, among different contrasting soil types. Additionally, the abundance of community members was assessed by quantifying the gene copy numbers for 16S rRNA, cbbL, cbbM, apsA and soxB. Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling, such as Gammaproteobacteria (Thiohalomonas, Allochromatium, Chromatium, Thiomicrospira) and Alphaproteobacteria (Rhodopseudomonas, Rhodovulum, Paracoccus). The rhizosphere soil was devoid of sulphur metabolism, as the soxB and apsA genes were not observed in the rhizosphere metagenome, which suggests the absence or inadequate representation of sulphur-oxidising bacteria. We hypothesise that the novel Gammaproteobacteria sulphur oxidisers might be actively involved in sulphur oxidation and inorganic carbon fixation, particularly in barren saline soil ecosystems, suggesting their significant putative ecological role and contribution to the soil carbon pool. PMID:25225969

Unravelling the carbon and sulphur metabolism in coastal soil ecosystems using comparative cultivation-independent genome-level characterisation of microbial communities.

PubMed

Yousuf, Basit; Kumar, Raghawendra; Mishra, Avinash; Jha, Bhavanath

2014-01-01

Bacterial autotrophy contributes significantly to the overall carbon balance, which stabilises atmospheric CO2 concentration and decelerates global warming. Little attention has been paid to different modes of carbon/sulphur metabolism mediated by autotrophic bacterial communities in terrestrial soil ecosystems. We studied these pathways by analysing the distribution and abundance of the diagnostic metabolic marker genes cbbM, apsA and soxB, which encode for ribulose-1,5-bisphosphate carboxylase/oxygenase, adenosine phosphosulphate reductase and sulphate thiohydrolase, respectively, among different contrasting soil types. Additionally, the abundance of community members was assessed by quantifying the gene copy numbers for 16S rRNA, cbbL, cbbM, apsA and soxB. Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling, such as Gammaproteobacteria (Thiohalomonas, Allochromatium, Chromatium, Thiomicrospira) and Alphaproteobacteria (Rhodopseudomonas, Rhodovulum, Paracoccus). The rhizosphere soil was devoid of sulphur metabolism, as the soxB and apsA genes were not observed in the rhizosphere metagenome, which suggests the absence or inadequate representation of sulphur-oxidising bacteria. We hypothesise that the novel Gammaproteobacteria sulphur oxidisers might be actively involved in sulphur oxidation and inorganic carbon fixation, particularly in barren saline soil ecosystems, suggesting their significant putative ecological role and contribution to the soil carbon pool.

Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications.

PubMed Central

Fetzner, S; Lingens, F

1994-01-01

This review is a survey of bacterial dehalogenases that catalyze the cleavage of halogen substituents from haloaromatics, haloalkanes, haloalcohols, and haloalkanoic acids. Concerning the enzymatic cleavage of the carbon-halogen bond, seven mechanisms of dehalogenation are known, namely, reductive, oxygenolytic, hydrolytic, and thiolytic dehalogenation; intramolecular nucleophilic displacement; dehydrohalogenation; and hydration. Spontaneous dehalogenation reactions may occur as a result of chemical decomposition of unstable primary products of an unassociated enzyme reaction, and fortuitous dehalogenation can result from the action of broad-specificity enzymes converting halogenated analogs of their natural substrate. Reductive dehalogenation either is catalyzed by a specific dehalogenase or may be mediated by free or enzyme-bound transition metal cofactors (porphyrins, corrins). Desulfomonile tiedjei DCB-1 couples energy conservation to a reductive dechlorination reaction. The biochemistry and genetics of oxygenolytic and hydrolytic haloaromatic dehalogenases are discussed. Concerning the haloalkanes, oxygenases, glutathione S-transferases, halidohydrolases, and dehydrohalogenases are involved in the dehalogenation of different haloalkane compounds. The epoxide-forming halohydrin hydrogen halide lyases form a distinct class of dehalogenases. The dehalogenation of alpha-halosubstituted alkanoic acids is catalyzed by halidohydrolases, which, according to their substrate and inhibitor specificity and mode of product formation, are placed into distinct mechanistic groups. beta-Halosubstituted alkanoic acids are dehalogenated by halidohydrolases acting on the coenzyme A ester of the beta-haloalkanoic acid. Microbial systems offer a versatile potential for biotechnological applications. Because of their enantiomer selectivity, some dehalogenases are used as industrial biocatalysts for the synthesis of chiral compounds. The application of dehalogenases or bacterial

Engineered Salmonella enterica serovar Typhimurium overcomes limitations of anti-bacterial immunity in bacteria-mediated tumor therapy

PubMed Central

Felgner, Sebastian; Kocijancic, Dino; Frahm, Michael; Heise, Ulrike; Rohde, Manfred; Zimmermann, Kurt; Falk, Christine; Weiss, Siegfried

2018-01-01

ABSTRACT Cancer is one of the leading causes of death in the industrialized world and represents a tremendous social and economic burden. As conventional therapies fail to provide a sustainable cure for most cancer patients, the emerging unique immune therapeutic approach of bacteria-mediated tumor therapy (BMTT) is marching towards a feasible solution. Although promising results have been obtained with BMTT using various preclinical tumor models, for advancement a major concern is immunity against the bacterial vector itself. Pre-exposure to the therapeutic agent under field conditions is a reasonable expectation and may limit the therapeutic efficacy of BMTT. In the present study, we investigated the therapeutic potential of Salmonella and E. coli vector strains in naïve and immunized tumor bearing mice. Pre-exposure to the therapeutic agent caused a significant aberrant phenotype of the microenvironment of colonized tumors and limited the in vivo efficacy of established BMTT vector strains Salmonella SL7207 and E. coli Symbioflor-2. Using targeted genetic engineering, we generated the optimized auxotrophic Salmonella vector strain SF200 (ΔlpxR9 ΔpagL7 ΔpagP8 ΔaroA ΔydiV ΔfliF) harboring modifications in Lipid A and flagella synthesis. This combination of mutations resulted in an increased immune-stimulatory capacity and as such the strain was able to overcome the efficacy-limiting effects of pre-exposure. Thus, we conclude that any limitations of BMTT concerning anti-bacterial immunity may be countered by strategies that optimize the immune-stimulatory capacity of the attenuated vector strains. PMID:29308303

Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

PubMed Central

Logue, Jürg B; Stedmon, Colin A; Kellerman, Anne M; Nielsen, Nikoline J; Andersson, Anders F; Laudon, Hjalmar; Lindström, Eva S; Kritzberg, Emma S

2016-01-01

Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance. PMID:26296065

Metagenomic insights into zooplankton‐associated bacterial communities

PubMed Central

Srivastava, Abhishek; Koski, Marja; Garcia, Juan Antonio L.; Takaki, Yoshihiro; Yokokawa, Taichi; Nunoura, Takuro; Elisabeth, Nathalie H.; Sintes, Eva; Herndl, Gerhard J.

2017-01-01

Summary Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton‐associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton‐associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton‐associated microbiome suggests that this zooplankton‐associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. PMID:28967193

Protein-Mediated Precipitation of Calcium Carbonate

PubMed Central

Polowczyk, Izabela; Bastrzyk, Anna; Fiedot, Marta

2016-01-01

Calcium carbonate is an important component in exoskeletons of many organisms. The synthesis of calcium carbonate was performed by mixing dimethyl carbonate and an aqueous solution of calcium chloride dihydrate. The precipitation product was characterized by means of scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR) measurements. In addition, the turbidity of the reaction solution was acquired to monitor the kinetics of the calcium carbonate structure’s growth in the investigated system. In this study, samples of CaCO3 particles obtained with individual proteins, such as ovalbumin, lysozyme, and a mixture of the proteins, were characterized and compared with a control sample, i.e., synthesized without proteins. The obtained data indicated that the addition of ovalbumin to the reaction changed the morphology of crystals from rhombohedral to ‘stack-like’ structures. Lysozyme, however, did not affect the morphology of calcium carbonate, yet the presence of the protein mixture led to the creation of more complex composites in which the calcium carbonate crystals were constructed in protein matrices formed by the ovalbumin-lysozyme interaction. It was also observed that in the protein mixture, ovalbumin has a major influence on the CaCO3 formation through a strong interaction with calcium ions, which leads to the coalescence and creation of a steric barrier reducing particle growth. The authors proposed a mechanism of calcium carbonate grain growth in the presence of both proteins, taking into account the interaction of calcium ions with the protein. PMID:28774065

Functioned silver nanoparticle loaded activated carbon for the recovery of bioactive molecule from bacterial fermenter for its bactericidal activity

NASA Astrophysics Data System (ADS)

Arivizhivendhan, Villalan; Mahesh, Mannacharaju; Boopathy, Ramasamy; Karthikeyan, Sekar; Mary, Rathanasamy Regina; Sekaran, Ganesan

2018-01-01

A novel continuous production and extraction of bacterial bioactive prodigiosin (PG) from fermented using silver nanoparticle impregnated functioned activated carbon composite is proposed for cost-effective and ecofriendly microbial technique. Hence, in this investigation silver nanoparticle was impregnated onto functioned activated carbon ([AC]F) as a support matrix and to enable the separation of PG conjugated silver nanoparticle from the fermented medium. A laboratory scale experiment was carried out to evaluate the continuous production and recovery of PG using [AC@Ag]F. Ag nanoparticle impregnated [AC]F ([AC@Ag]F) characterized by FT-IR, XRD, TGA, DSC and SEM. Instrumental analyses confirmed that Ag nanoparticles significantly impregnated on AC through the functionalization of AC with diethanolamine and it enhances the binding capacity between AC and Ag. The various process parameters, such as contact time, pH, and mass of [AC@Ag]F, were statistically optimized for the recovery of PG using Response Surface Methodology (RSM). The maximum extraction of PG in [AC@Ag]F was found to be 16.2 ± 0.2 mg g-1, its twofold higher than [AC]F. Further, PG conjugated [AC@Ag]F and ([AC@Ag]F-PG) were checked for the growth inhibition of gram negative and gram positive bacteria without formation of biofilm upto 96 h. Hence, the developed matrix could be eco-friendly, viable and lower energy consumption step for separation of the bacterial bioactive PG from fermented broth. In additionally, [AC@Ag]F-PG was used as an antifouling matrix without formation of biofilm.

The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

PubMed Central

Hope Wilkinson, Katheryn; Strait, Jacqueline M.; Hozalski, Raymond M.; Sadowksy, Michael J.; Hamilton, Matthew J.

2015-01-01

The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB. PMID:26209671

Iron-mediated soil carbon response to water-table decline in an alpine wetland

PubMed Central

Wang, Yiyun; Wang, Hao; He, Jin-Sheng; Feng, Xiaojuan

2017-01-01

The tremendous reservoir of soil organic carbon (SOC) in wetlands is being threatened by water-table decline (WTD) globally. However, the SOC response to WTD remains highly uncertain. Here we examine the under-investigated role of iron (Fe) in mediating soil enzyme activity and lignin stabilization in a mesocosm WTD experiment in an alpine wetland. In contrast to the classic ‘enzyme latch’ theory, phenol oxidative activity is mainly controlled by ferrous iron [Fe(II)] and declines with WTD, leading to an accumulation of dissolvable aromatics and a reduced activity of hydrolytic enzyme. Furthermore, using dithionite to remove Fe oxides, we observe a significant increase of Fe-protected lignin phenols in the air-exposed soils. Fe oxidation hence acts as an ‘iron gate’ against the ‘enzyme latch’ in regulating wetland SOC dynamics under oxygen exposure. This newly recognized mechanism may be key to predicting wetland soil carbon storage with intensified WTD in a changing climate. PMID:28649988

Iron-mediated soil carbon response to water-table decline in an alpine wetland

NASA Astrophysics Data System (ADS)

Wang, Yiyun; Wang, Hao; He, Jin-Sheng; Feng, Xiaojuan

2017-06-01

The tremendous reservoir of soil organic carbon (SOC) in wetlands is being threatened by water-table decline (WTD) globally. However, the SOC response to WTD remains highly uncertain. Here we examine the under-investigated role of iron (Fe) in mediating soil enzyme activity and lignin stabilization in a mesocosm WTD experiment in an alpine wetland. In contrast to the classic `enzyme latch' theory, phenol oxidative activity is mainly controlled by ferrous iron [Fe(II)] and declines with WTD, leading to an accumulation of dissolvable aromatics and a reduced activity of hydrolytic enzyme. Furthermore, using dithionite to remove Fe oxides, we observe a significant increase of Fe-protected lignin phenols in the air-exposed soils. Fe oxidation hence acts as an `iron gate' against the `enzyme latch' in regulating wetland SOC dynamics under oxygen exposure. This newly recognized mechanism may be key to predicting wetland soil carbon storage with intensified WTD in a changing climate.

BAC to degeneration bacterial artificial chromosome (BAC)-mediated transgenesis for modeling basal ganglia neurodegenerative disorders.

PubMed

Lu, Xiao-Hong

2009-01-01

Basal ganglia neurodegenerative disorders, such as Parkinson's disease (PD) and Huntington's disease (HD), are characterized by not only spectrum of motor deficits, ranging form hypokinesia to hyperkinesia, but also emotional, cognitive, and psychiatric manifestations. The symptoms and pathogenic mechanism of these disorders should be viewed as dysfunctions of specific cortico-subcortical neurocircuits. Transgenic approaches using large genomic inserts, such as bacterial artificial chromosome (BAC)-mediated transgenesis, due to its capacity to propagate large-size genomic DNA and faithful production of endogenous-like gene expression pattern/lever, have provided an ideal basis for the generation of transgenic mice as model for basal ganglia neurodegenerative disorders, as well as the functional and structural analysis of neurocircuits. In this chapter, the basic concepts and practical approaches about application of BAC transgenic system are introduced. Existent major BAC transgenic mouse models for PD and HD are evaluated according to their construct, face, and predicative validity. Finally, considerations, possible solutions, and future perspectives of using BAC transgenic approach to study basal ganglia neurodegenerative disorders are discussed.

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder

PubMed Central

Carrick, Hunter J.; Cavaletto, Joann; Chiang, Edna; Johengen, Thomas H.; Vanderploeg, Henry A.

2017-01-01

ABSTRACT One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptible to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions. IMPORTANCE Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder.

PubMed

Denef, Vincent J; Carrick, Hunter J; Cavaletto, Joann; Chiang, Edna; Johengen, Thomas H; Vanderploeg, Henry A

2017-01-01

One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptible to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions. IMPORTANCE Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Denef, Vincent J.; Carrick, Hunter J.; Cavaletto, Joann

One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptiblemore » to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions.Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder

DOE PAGES

Denef, Vincent J.; Carrick, Hunter J.; Cavaletto, Joann; ...

2017-05-31

One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptiblemore » to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions.Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of

New target for inhibition of bacterial RNA polymerase: 'switch region'.

PubMed

Srivastava, Aashish; Talaue, Meliza; Liu, Shuang; Degen, David; Ebright, Richard Y; Sineva, Elena; Chakraborty, Anirban; Druzhinin, Sergey Y; Chatterjee, Sujoy; Mukhopadhyay, Jayanta; Ebright, Yon W; Zozula, Alex; Shen, Juan; Sengupta, Sonali; Niedfeldt, Rui Rong; Xin, Cai; Kaneko, Takushi; Irschik, Herbert; Jansen, Rolf; Donadio, Stefano; Connell, Nancy; Ebright, Richard H

2011-10-01

A new drug target - the 'switch region' - has been identified within bacterial RNA polymerase (RNAP), the enzyme that mediates bacterial RNA synthesis. The new target serves as the binding site for compounds that inhibit bacterial RNA synthesis and kill bacteria. Since the new target is present in most bacterial species, compounds that bind to the new target are active against a broad spectrum of bacterial species. Since the new target is different from targets of other antibacterial agents, compounds that bind to the new target are not cross-resistant with other antibacterial agents. Four antibiotics that function through the new target have been identified: myxopyronin, corallopyronin, ripostatin, and lipiarmycin. This review summarizes the switch region, switch-region inhibitors, and implications for antibacterial drug discovery. Copyright © 2011 Elsevier Ltd. All rights reserved.

5-Aminoimidazole-4-carboxamide ribonucleoside-mediated adenosine monophosphate-activated protein kinase activation induces protective innate responses in bacterial endophthalmitis.

PubMed

Kumar, Ajay; Giri, Shailendra; Kumar, Ashok

2016-12-01

The retina is considered to be the most metabolically active tissue in the body. However, the link between energy metabolism and retinal inflammation, as incited by microbial infection such as endophthalmitis, remains unexplored. In this study, using a mouse model of Staphylococcus aureus (SA) endophthalmitis, we demonstrate that the activity (phosphorylation) of 5' adenosine monophosphate-activated protein kinase alpha (AMPKα), a cellular energy sensor and its endogenous substrate; acetyl-CoA carboxylase is down-regulated in the SA-infected retina. Intravitreal administration of an AMPK activator, 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR), restored AMPKα and acetyl-CoA carboxylase phosphorylation. AICAR treatment reduced both the bacterial burden and intraocular inflammation in SA-infected eyes by inhibiting NF-kB and MAP kinases (p38 and JNK) signalling. The anti-inflammatory effects of AICAR were diminished in eyes pretreated with AMPK inhibitor, Compound C. The bioenergetics (Seahorse) analysis of SA-infected microglia and bone marrow-derived macrophages revealed an increase in glycolysis, which was reinstated by AICAR treatment. AICAR also reduced the expression of SA-induced glycolytic genes, including hexokinase 2 and glucose transporter 1 in microglia, bone marrow-derived macrophages and the mouse retina. Interestingly, AICAR treatment enhanced the bacterial phagocytic and intracellular killing activities of cultured microglia, macrophages and neutrophils. Furthermore, AMPKα1 global knockout mice exhibited increased susceptibility towards SA endophthalmitis, as evidenced by increased inflammatory mediators and bacterial burden and reduced retinal function. Together, these findings provide the first evidence that AMPK activation promotes retinal innate defence in endophthalmitis by modulating energy metabolism and that it can be targeted therapeutically to treat ocular infections. © 2016 John Wiley & Sons Ltd.

Biosynthesis of Bacterial Cellulose/Carboxylic Multi-Walled Carbon Nanotubes for Enzymatic Biofuel Cell Application

PubMed Central

Lv, Pengfei; Feng, Quan; Wang, Qingqing; Li, Guohui; Li, Dawei; Wei, Qufu

2016-01-01

Novel nanocomposites comprised of bacterial cellulose (BC) with carboxylic multi-walled carbon nanotubes (c-MWCNTs) incorporated into the BC matrix were prepared through a simple method of biosynthesis. The biocathode and bioanode for the enzyme biological fuel cell (EBFC) were prepared using BC/c-MWCNTs composite injected by laccase (Lac) and glucose oxidase (GOD) with the aid of glutaraldehyde (GA) crosslinking. Biosynthesis of BC/c-MWCNTs composite was characterized by digital photos, scanning electron microscope (SEM), and Fourier Transform Infrared (FTIR). The experimental results indicated the successful incorporation of c-MWCNTs into the BC. The electrochemical and biofuel performance were evaluated by cyclic voltammetry (CV) and linear sweep voltammetry (LSV). The power density and current density of EBFCs were recorded at 32.98 µW/cm3 and 0.29 mA/cm3, respectively. Additionally, the EBFCs also showed acceptable stability. Preliminary tests on double cells indicated that renewable BC have great potential in the application field of EBFCs. PMID:28773310

New evidence for Cu-decorated binary-oxides mediating bacterial inactivation/mineralization in aerobic media.

PubMed

Rtimi, S; Pulgarin, C; Bensimon, M; Kiwi, J

2016-08-01

Binary oxide semiconductors TiO2-ZrO2 and Cu-decorated TiO2-ZrO2 (TiO2-ZrO2-Cu) uniform films were sputtered on polyester (PES). These films were irradiated under low intensity solar simulated light and led to bacterial inactivation in aerobic and anaerobic media as evaluated by CFU-plate counting. But bacterial mineralization was only induced by TiO2-ZrO2-Cu in aerobic media. The highly oxidative radicals generated on the films surface under light were identified by the use of appropriate scavengers. The hole generated on the TiO2-ZrO2 films is shown to be the main specie leading to bacterial inactivation. TiO2-ZrO2 and Cu-decorated TiO2-ZrO2 films release Zr and Ti <1ppb and Cu 4.6ppb/cm(2) as determined by inductively coupled plasma mass spectrometry (ICP-MS) This level is far below the citotoxicity permitted level allowed for mammalian cells suggesting that bacterial disinfection proceeds through an oligodynamic effect. By Fourier transform attenuated infrared spectroscopy (ATR-FTIR) the systematic shift of the predominating νs(CH2) vibrational-rotational peak making up most of the bacterial cell-wall content in C was monitored. Based on this evidence a mechanism suggested leading to CH bond stretching followed by cell lysis and cell death. Bacterial inactivation cycling was observed on TiO2-ZrO2-Cu showing the stability of these films leading to bacterial inactivation. Copyright © 2016 Elsevier B.V. All rights reserved.

Macroalgal-bacterial interactions: Role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta).

PubMed

Kessler, Ralf W; Weiss, Anne; Kuegler, Stefan; Hermes, Cornelia; Wichard, Thomas

2018-04-01

The marine macroalga Ulva mutabilis (Chlorophyta) develops into callus-like colonies consisting of undifferentiated cells and abnormal cell walls under axenic conditions. Ulva mutabilis is routinely cultured with two bacteria, the Roseovarius sp. MS2 strain and the Maribacter sp. MS6 strain, which release morphogenetic compounds and ensure proper algal morphogenesis. Using this tripartite community as an emerging model system, we tested the hypothesis that the bacterial-algal interactions evolved as a result of mutually taking advantage of signals in the environment. Our study aimed to determine whether cross-kingdom crosstalk is mediated by the attraction of bacteria through algal chemotactic signals. Roseovarius sp. MS2 senses the known osmolyte dimethylsulfoniopropionate (DMSP) released by Ulva into the growth medium. Roseovarius sp. is attracted by DMSP and takes it up rapidly such that DMSP can only be determined in axenic growth media. As DMSP did not promote bacterial growth under the tested conditions, Roseovarius benefited solely from glycerol as the carbon source provided by Ulva. Roseovarius quickly catabolized DMSP into methanethiol (MeSH) and dimethylsulphide (DMS). We conclude that many bacteria can use DMSP as a reliable signal indicating a food source and promote the subsequent development and morphogenesis in Ulva. © 2017 John Wiley & Sons Ltd.

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes.

PubMed

Zhang, Yuanchen; Kastman, Erik K; Guasto, Jeffrey S; Wolfe, Benjamin E

2018-01-23

Most studies of bacterial motility have examined small-scale (micrometer-centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes.

Inhibition of bacterial carbonic anhydrases and zinc proteases: from orphan targets to innovative new antibiotic drugs.

PubMed

Supuran, C T

2012-01-01

Zinc-containing enzymes, such as carbonic anhydrases (CAs) and metalloproteases (MPs) play critical functions in bacteria, being involved in various steps of their life cycle, which are important for survival, colonization, acquisition of nutrients for growth and proliferation, facilitation of dissemination, invasion and pathogenicity. The development of resistance to many classes of clinically used antibiotics emphasizes the need of new antibacterial drug targets to be explored. There is a wealth of data regarding bacterial CAs and zinc MPs present in many pathogenic species, such as Neisseria spp., Helycobacter pylori Escherichia coli, Mycobacterium tuberculosis, Brucella spp., Streptococcus pneumoniae, Salmonella enterica, Haemophilus influenzae, Listeria spp, Vibrio spp., Pseudomonas aeruginosa, Legionella pneumophila, Streptomyces spp., Clostridium spp., Enterococcus spp., etc. Some of these enzymes have been cloned, purified and characterized by crystallographic techniques. However, for the moment, few potent and specific inhibitors for bacterial MPs have been reported except for Clostridium histolyticum collagenase, botulinum and tetanus neurotoxin and anthrax lethal factor, which will be reviewed in this article. Bacteria encode α-,β-, and/or γ-CA families, but up to now only the first two classes have been investigated in some detail in different species. The α-CAs from Neisseria spp. and H. pylori as well as the β-class enzymes from E. coli, H. pylori, M. tuberculosis, Brucella spp., S. pneumoniae, S. enterica and H. influenzae have been cloned and characterized. The catalytic/inhibition mechanisms of these CAs are well understood as X-ray crystal structures are available for some of them, but no adducts of these enzymes with inhibitors have been characterized so far. In vitro and in vivo studies with various classes of inhibitors, such as anions, sulfonamides and sulfamates have been reported. Only for Neisseria spp., H. pylori, B. suis and S

Inhibition of bacterial and leukocyte adhesion under shear stress conditions by material surface chemistry.

PubMed

Patel, Jasmine D; Ebert, Michael; Stokes, Ken; Ward, Robert; Anderson, James M

2003-01-01

Biomaterial-centered infections, initiated by bacterial adhesion, persist due to a compromised host immune response. Altering implant materials with surface modifying endgroups (SMEs) may enhance their biocompatibility by reducing bacterial and inflammatory cell adhesion. A rotating disc model, which generates shear stress within physiological ranges, was used to characterize adhesion of leukocytes and Staphylococcus epidermidis on polycarbonate-urethanes and polyetherurethanes modified with SMEs (polyethylene oxide, fluorocarbon and dimethylsiloxane) under dynamic flow conditions. Bacterial adhesion in the absence of serum was found to be mediated by shear stress and surface chemistry, with reduced adhesion exhibited on materials modified with polydimethylsiloxane and polyethylene oxide SMEs. In contrast, bacterial adhesion was enhanced on materials modified with fluorocarbon SMEs. In the presence of serum, bacterial adhesion was primarily neither material nor shear dependent. However, bacterial adhesion in serum was significantly reduced to < or = 10% compared to adhesion in serum-free media. Leukocyte adhesion in serum exhibited a shear dependency with increased adhesion occurring in regions exposed to lower shear-stress levels of < or = 7 dyne/cm2. Additionally, polydimethylsiloxane and polyethylene oxide SMEs reduced leukocyte adhesion on polyether-urethanes. In conclusion, these results suggest that surface chemistry and shear stress can mediate bacterial and cellular adhesion. Furthermore, materials modified with polyethylene oxide SMEs are capable of inhibiting bacterial adhesion, consequently minimizing the probability of biomaterial-centered infections.

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community.

PubMed

Hortal, S; Lozano, Y M; Bastida, F; Armas, C; Moreno, J L; Garcia, C; Pugnaire, F I

2017-12-19

Competition is a key process that determines plant community structure and dynamics, often mediated by nutrients and water availability. However, the role of soil microorganisms on plant competition, and the links between above- and belowground processes, are not well understood. Here we show that the effects of interspecific plant competition on plant performance are mediated by feedbacks between plants and soil bacterial communities. Each plant species selects a singular community of soil microorganisms in its rhizosphere with a specific species composition, abundance and activity. When two plant species interact, the resulting soil bacterial community matches that of the most competitive plant species, suggesting strong competitive interactions between soil bacterial communities as well. We propose a novel mechanism by which changes in belowground bacterial communities promoted by the most competitive plant species influence plant performance and competition outcome. These findings emphasise the strong links between plant and soil communities, paving the way to a better understanding of plant community dynamics and the effects of soil bacterial communities on ecosystem functioning and services.

Characterization of bacterial diversity associated with calcareous deposits and drip-waters, and isolation of calcifying bacteria from two Colombian mines.

PubMed

García G, Mariandrea; Márquez G, Marco Antonio; Moreno H, Claudia Ximena

2016-01-01

Bacterial carbonate precipitation has implications in geological processes and important biotechnological applications. Bacteria capable of precipitating carbonates have been isolated from different calcium carbonate deposits (speleothems) in caves, soil, freshwater and seawater around the world. However, the diversity of bacteria from calcareous deposits in Colombia, and their ability to precipitate carbonates, remains unknown. In this study, conventional microbiological methods and molecular tools, such as temporal temperature gradient electrophoresis (TTGE), were used to assess the composition of bacterial communities associated with carbonate deposits and drip-waters from two Colombian mines. A genetic analysis of these bacterial communities revealed a similar level of diversity, based on the number of bands detected using TTGE. The dominant phylogenetic affiliations of the bacteria, determined using 16S rRNA gene sequencing, were grouped into two phyla: Proteobacteria and Firmicutes. Within these phyla, seven genera were capable of precipitating calcium carbonates: Lysinibacillus, Bacillus, Strenotophomonas, Brevibacillus, Methylobacterium, Aeromicrobium and Acinetobacter. FTIR and SEM/EDX were used to analyze calcium carbonate crystals produced by isolated Acinetobacter gyllenbergii. The results showed that rhombohedral and angular calcite crystals with sizes of 90μm were precipitated. This research provides information regarding the presence of complex bacterial communities in secondary carbonate deposits from mines and their ability to precipitate calcium carbonate from calcareous deposits of Colombian mines. Copyright © 2015 Elsevier GmbH. All rights reserved.

Bacterial Genome Instability

PubMed Central

Darmon, Elise

2014-01-01

SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease. PMID:24600039

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Zilian; Chen, Yi; Wang, Rui

Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not bemore » completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. Finally, the fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.« less

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

DOE PAGES

Zhang, Zilian; Chen, Yi; Wang, Rui; ...

2015-11-16

Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not bemore » completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. Finally, the fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.« less

Cerebral blood flow and carbon dioxide reactivity in children with bacterial meningitis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ashwal, S.; Stringer, W.; Tomasi, L.

1990-10-01

We examined total and regional cerebral blood flow (CBF) by stable xenon computed tomography in 20 seriously ill children with acute bacterial meningitis to determine whether CBF was reduced and to examine the changes in CBF during hyperventilation. In 13 children, total CBF was normal (62 +/- 20 ml/min/100 gm) but marked local variability of flow was seen. In five other children, total CBF was significantly reduced (26 +/- 10 ml/min/100 gm; p less than 0.05), with flow reduced more in white matter (8 +/- 5 ml/min/100 gm) than in gray matter (30 +/- 15 ml/min/100 gm). Autoregulation of CBFmore » appeared to be present in these 18 children within a range of mean arterial blood pressure from 56 to 102 mm Hg. In the remaining two infants, brain dead within the first 24 hours, total flow was uniformly absent, averaging 3 +/- 3 ml/min/100 gm. In seven children, CBF was determined at two carbon dioxide tension (PCO2) levels: 40 (+/- 3) mm Hg and 29 (+/- 3) mm Hg. In six children, total CBF decreased 33%, from 52 (+/- 25) to 35 (+/- 15) ml/min/100 gm; the mean percentage of change in CBF per millimeter of mercury of PCO2 was 3.0%. Regional variability of perfusion to changes in PCO2 was marked in all six children. The percentage of change in CBF per millimeter of mercury of PCO2 was similar in frontal gray matter (3.1%) but higher in white matter (4.5%). In the seventh patient a paradoxical response was observed; total and regional CBF increased 25% after hyperventilation. Our findings demonstrate that (1) CBF in children with bacterial meningitis may be substantially decreased globally, with even more variability noted regionally, (2) autoregulation of CBF is preserved, (3) CBF/CO2 responsitivity varies among patients and in different regions of the brain in the same patient, and (4) hyperventilation can reduce CBF below ischemic thresholds.« less

Macrofauna regulate heterotrophic bacterial carbon and nitrogen incorporation in low-oxygen sediments

PubMed Central

Hunter, William R; Veuger, Bart; Witte, Ursula

2012-01-01

Oxygen minimum zones (OMZs) currently impinge upon >1 million km2 of sea floor and are predicted to expand with climate change. We investigated how changes in oxygen availability, macrofaunal biomass and retention of labile organic matter (OM) regulate heterotrophic bacterial C and N incorporation in the sediments of the OMZ-impacted Indian continental margin (540–1100 m; [O2]=0.35–15 μmol l−1). In situ pulse-chase experiments traced 13C:15N-labelled phytodetritus into bulk sediment OM and hydrolysable amino acids, including the bacterial biomarker 𝒟-alanine. Where oxygen availability was lowest ([O2]=0.35 μmol l−1), metazoan macrofauna were absent and bacteria assimilated 30–90% of the labelled phytodetritus within the sediment. At higher oxygen levels ([O2]=2–15 μmol l−1) the macrofaunal presence and lower phytodetritus retention with the sediment occur concomitantly, and bacterial phytodetrital incorporation was reduced and retarded. Bacterial C and N incorporation exhibited a significant negative relationship with macrofaunal biomass across the OMZ. We hypothesise that fauna–bacterial interactions significantly influence OM recycling in low-oxygen sediments and need to be considered when assessing the consequences of global change on biogeochemical cycles. PMID:22592818

Combining stable isotope isotope geochemistry and carbonic anhydrase activity to trace vital effect in carbonate precipitation experiments

NASA Astrophysics Data System (ADS)

Thaler, C.; Ader, M.; Menez, B.; Guyot, F. J.

2013-12-01

Carbonates precipitated by skeleton-forming eukaryotic organisms are often characterized by non-equilibrium isotopic signatures. This specificity is referred to as the "vital effect" and can be used as an isotopic evidence to trace life. Combining stable isotope geochemistry and enzymology (using the enzyme carbonic anhydrase) we aim to demonstrate that prokaryotes are also able to precipitate carbonate with a non-equilibrium d18OCaCO3. Indeed, if in an biomineralization experiment carbonates are precipitated with a vital effect, the addition of carbonic anhydrase should drive the system to isotope equilibrium, And provide a comparison point to estimate the vital effect range. This protocol allowed us to identify a -20‰ vital effect for the d18O of carbonates precipitated by Sporosarcina pasteurii, a bacterial model of carbonatogen metabolisms. This approach is thus a powerfull tool for the understanding of microbe carbonatogen activity and will probably bring new insights into the understanding of bacterial activity in subsurface and during diagenesis.

Cell shape can mediate the spatial organization of the bacterial cytoskeleton

NASA Astrophysics Data System (ADS)

Wang, Siyuan; Wingreen, Ned

2013-03-01

The bacterial cytoskeleton guides the synthesis of cell wall and thus regulates cell shape. Since spatial patterning of the bacterial cytoskeleton is critical to the proper control of cell shape, it is important to ask how the cytoskeleton spatially self-organizes in the first place. In this work, we develop a quantitative model to account for the various spatial patterns adopted by bacterial cytoskeletal proteins, especially the orientation and length of cytoskeletal filaments such as FtsZ and MreB in rod-shaped cells. We show that the combined mechanical energy of membrane bending, membrane pinning, and filament bending of a membrane-attached cytoskeletal filament can be sufficient to prescribe orientation, e.g. circumferential for FtsZ or helical for MreB, with the accuracy of orientation increasing with the length of the cytoskeletal filament. Moreover, the mechanical energy can compete with the chemical energy of cytoskeletal polymerization to regulate filament length. Notably, we predict a conformational transition with increasing polymer length from smoothly curved to end-bent polymers. Finally, the mechanical energy also results in a mutual attraction among polymers on the same membrane, which could facilitate tight polymer spacing or bundling. The predictions of the model can be verified through genetic, microscopic, and microfluidic approaches.

Capsule Polysaccharide Mediates Bacterial Resistance to Antimicrobial Peptides

PubMed Central

Campos, Miguel A.; Vargas, Miguel A.; Regueiro, Verónica; Llompart, Catalina M.; Albertí, Sebastián; Bengoechea, José A.

2004-01-01

The innate immune system plays a critical role in the defense of areas exposed to microorganisms. There is an increasing body of evidence indicating that antimicrobial peptides and proteins (APs) are one of the most important weapons of this system and that they make up the protective front for the respiratory tract. On the other hand, it is known that pathogenic organisms have developed countermeasures to resist these agents such as reducing the net negative charge of the bacterial membranes. Here we report the characterization of a novel mechanism of resistance to APs that is dependent on the bacterial capsule polysaccharide (CPS). Klebsiella pneumoniae CPS mutant was more sensitive than the wild type to human neutrophil defensin 1, β-defensin 1, lactoferrin, protamine sulfate, and polymyxin B. K. pneumoniae lipopolysaccharide O antigen did not play an important role in AP resistance, and CPS was the only factor conferring protection against polymyxin B in strains lacking O antigen. In addition, we found a significant correlation between the amount of CPS expressed by a given strain and the resistance to polymyxin B. We also showed that K. pneumoniae CPS mutant bound more polymyxin B than the wild-type strain with a concomitant increased in the self-promoted pathway. Taken together, our results suggest that CPS protects bacteria by limiting the interaction of APs with the surface. Finally, we report that K. pneumoniae increased the amount of CPS and upregulated cps transcription when grown in the presence of polymyxin B and lactoferrin. PMID:15557634

Analysis of the Binding Moiety Mediating the Interaction between Monocarboxylate Transporters and Carbonic Anhydrase II*

PubMed Central

Noor, Sina Ibne; Dietz, Steffen; Heidtmann, Hella; Boone, Christopher D.; McKenna, Robert; Deitmer, Joachim W.; Becker, Holger M.

2015-01-01

Proton-coupled monocarboxylate transporters (MCTs) mediate the exchange of high energy metabolites like lactate between different cells and tissues. We have reported previously that carbonic anhydrase II augments transport activity of MCT1 and MCT4 by a noncatalytic mechanism, while leaving transport activity of MCT2 unaltered. In the present study, we combined electrophysiological measurements in Xenopus oocytes and pulldown experiments to analyze the direct interaction between carbonic anhydrase II (CAII) and MCT1, MCT2, and MCT4, respectively. Transport activity of MCT2-WT, which lacks a putative CAII-binding site, is not augmented by CAII. However, introduction of a CAII-binding site into the C terminus of MCT2 resulted in CAII-mediated facilitation of MCT2 transport activity. Interestingly, introduction of three glutamic acid residues alone was not sufficient to establish a direct interaction between MCT2 and CAII, but the cluster had to be arranged in a fashion that allowed access to the binding moiety in CAII. We further demonstrate that functional interaction between MCT4 and CAII requires direct binding of the enzyme to the acidic cluster 431EEE in the C terminus of MCT4 in a similar fashion as previously shown for binding of CAII to the cluster 489EEE in the C terminus of MCT1. In CAII, binding to MCT1 and MCT4 is mediated by a histidine residue at position 64. Taken together, our results suggest that facilitation of MCT transport activity by CAII requires direct binding between histidine 64 in CAII and a cluster of glutamic acid residues in the C terminus of the transporter that has to be positioned in surroundings that allow access to CAII. PMID:25561737

PGE2 suppresses intestinal T cell function in thermal injury: a cause of enhanced bacterial translocation.

PubMed

Choudhry, M A; Fazal, N; Namak, S Y; Haque, F; Ravindranath, T; Sayeed, M M

2001-09-01

Increased gut bacterial translocation in burn and trauma patients has been demonstrated in a number of previous studies, however, the mechanism for such an increased gut bacterial translocation in injured patients remains poorly understood. Utilizing a rat model of burn injury, in the present study we examined the role of intestinal immune defense by analyzing the T cell functions. We investigated if intestinal T cells dysfunction contributes to bacterial translocation after burn injury. Also our study determined if burn-mediated alterations in intestinal T cell functions are related to enhanced release of PGE2. Finally, we examined whether or not burn-related alterations in intestinal T cell function are due to inappropriate activation of signaling molecule P59fyn, which is required for T cell activation and proliferation. The results presented here showed an increase in gut bacterial accumulation in mesenteric lymph nodes after thermal injury. This was accompanied by a decrease in the intestinal T cell proliferative responses. Furthermore, the treatments of burn-injured animals with PGE2 synthesis blocker (indomethacin or NS398) prevented both the decrease in intestinal T cell proliferation and enhanced bacterial translocation. Finally, our data suggested that the inhibition of intestinal T cell proliferation could result via PGE2-mediated down-regulation of the T cell activation-signaling molecule P59fyn. These findings support a role of T cell-mediated immune defense against bacterial translocation in burn injury.

Bacterial brown leaf spot of citrus, a new disease caused by Burkholderia andropogonis

USDA-ARS?s Scientific Manuscript database

A new bacterial disease of citrus was recently identified in Florida and named as bacterial brown leaf spot (BBLS) of citrus. BBLS-infected citrus displayed flat, circular and brownish lesions with water-soaked margins surrounded by a chlorotic halo on leaves. Based on Biolog carbon source metabolic...

Sub-second carbon-nanotube-mediated microwave sintering for high-conductivity silver patterns on plastic substrates

NASA Astrophysics Data System (ADS)

Jung, Sunshin; Chun, Su Jin; Han, Joong Tark; Woo, Jong Seok; Shon, Cha-Hwa; Lee, Geon-Woong

2016-02-01

A method of microwave sintering that is mediated by carbon nanotubes (CNTs) has been developed to obtain high-conductivity Ag patterns on the top of heat-sensitive plastic substrates within a short time. The Ag patterns are printed on CNTs formed on plastic substrates and rapidly heated to a great extent by the heat transferred from the microwave-heated CNTs. The conductivity of the microwave-sintered Ag patterns reaches ~39% that of bulk Ag within 1 s without substrate deformation. Furthermore, microwave sintering enhances the adhesion of Ag patterns to the thermoplastic substrates because the sintering causes interfacial fusion between the Ag patterns and the substrates, and CNTs physically connect the patterns with the substrates.A method of microwave sintering that is mediated by carbon nanotubes (CNTs) has been developed to obtain high-conductivity Ag patterns on the top of heat-sensitive plastic substrates within a short time. The Ag patterns are printed on CNTs formed on plastic substrates and rapidly heated to a great extent by the heat transferred from the microwave-heated CNTs. The conductivity of the microwave-sintered Ag patterns reaches ~39% that of bulk Ag within 1 s without substrate deformation. Furthermore, microwave sintering enhances the adhesion of Ag patterns to the thermoplastic substrates because the sintering causes interfacial fusion between the Ag patterns and the substrates, and CNTs physically connect the patterns with the substrates. Electronic supplementary information (ESI) available: Temperature difference in Ag/CNT/PC samples; the carbon content and electrical performance after microwave sintering; microwave sintering of Ag/CNT patterns; physical connection between the substrate and sintered Ag lines; touch-piano (figure and movie). See DOI: 10.1039/c5nr08082g

Bioorganic Fertilizer Enhances Soil Suppressive Capacity against Bacterial Wilt of Tomato

PubMed Central

Liu, Shuangri; Chai, Rushan; Huang, Weiqing; Liu, Xingxing; Tang, Caixian; Zhang, Yongsong

2015-01-01

Tomato bacterial wilt caused by Ralstonia solanacearum is one of the most destructive soil-borne diseases. Many strategies have been taken to improve soil suppressiveness against this destructive disease, but limited success has been achieved. In this study, a novel bioorganic fertilizer revealed a higher suppressive ability against bacterial wilt compared with several soil management methods in the field over four growing seasons from March 2011 to July 2013. The application of the bioorganic fertilizer significantly (P<0.05) reduced disease incidence of tomato and increased fruit yields in four independent trials. The association among the level of disease incidence, soil physicochemical and biological properties was investigated. The soil treated with the bioorganic fertilizer increased soil pH value, electric conductivity, organic carbon, NH4 +-N, NO3 --N and available K content, microbial activities and microbial biomass carbon content, which were positively related with soil suppressiveness. Bacterial and actinomycete populations assessed using classical plate counts were highest, whereas R. solanacearum and fungal populations were lowest in soil applied with the bioorganic fertilizer. Microbial community diversity and richness were assessed using denaturing gel gradient electrophoresis profile analysis. The soil treated with the bioorganic fertilizer exhibited higher bacterial community diversity but lower fungal community diversity. Redundancy analysis showed that bacterial community diversity and richness negatively related with bacterial wilt suppressiveness, while fungal community richness positively correlated with R. solanacearum population. We concluded that the alteration of soil physicochemical and biological properties in soil treated with the bioorganic fertilizer induced the soil suppressiveness against tomato bacterial wilt. PMID:25830639

Voltammetric Determination of Penicillamine Using a Carbon Paste Electrode Modified with Multiwall Carbon Nanotubes In the Presence of Methyldopa as a Mediator.

PubMed

Safari, Fardin; Keyvanfard, Mohsen; Karimi-Maleh, Hassan; Alizad, Khadijeh

2017-01-01

A multiwall carbon nanotubes-modified carbon paste electrode (MWCNTs/MCPE) was fabricated and used to study the electrooxidation of penicillamine (PA) by electrochemical methods in the presence of methyldopa (MDOP) as a homogeneous mediator. The electrochemical oxidation of PA on the new sensor has been carefully studied. The kinetic parameters such as electron transfer coefficient, α, and catalytic reaction rate constant, K / h , were also determined using electrochemical approaches. The electrocatalytic oxidation peak current of PA showed a linear dependent on the PA concentrations and linear calibration curves were obtained in the ranges of 0.2-250.0 µM of PA concentration with square wave voltammetry (SWV) method. The detection limit (3σ) was determined as 0.1 µM. This sensor was also examined as a fast, selective, simple and precise new sensor for voltammetric determination of PA in real samples such as drug and urine.

Voltammetric Determination of Penicillamine Using a Carbon Paste Electrode Modified with Multiwall Carbon Nanotubes In the Presence of Methyldopa as a Mediator

PubMed Central

Safari, Fardin; Keyvanfard, Mohsen; Karimi-Maleh, Hassan; Alizad, Khadijeh

2017-01-01

A multiwall carbon nanotubes-modified carbon paste electrode (MWCNTs/MCPE) was fabricated and used to study the electrooxidation of penicillamine (PA) by electrochemical methods in the presence of methyldopa (MDOP) as a homogeneous mediator. The electrochemical oxidation of PA on the new sensor has been carefully studied. The kinetic parameters such as electron transfer coefficient, α, and catalytic reaction rate constant, K/h, were also determined using electrochemical approaches. The electrocatalytic oxidation peak current of PA showed a linear dependent on the PA concentrations and linear calibration curves were obtained in the ranges of 0.2-250.0 µM of PA concentration with square wave voltammetry (SWV) method. The detection limit (3σ) was determined as 0.1 µM. This sensor was also examined as a fast, selective, simple and precise new sensor for voltammetric determination of PA in real samples such as drug and urine. PMID:29201090

Production and Reutilization of Fluorescent Dissolved Organic Matter by a Marine Bacterial Strain, Alteromonas macleodii

PubMed Central

Goto, Shuji; Tada, Yuya; Suzuki, Koji; Yamashita, Youhei

2017-01-01

The recalcitrant fraction of marine dissolved organic matter (DOM) plays an important role in carbon storage on the earth’s surface. Bacterial production of recalcitrant DOM (RDOM) has been proposed as a carbon sequestration process. It is still unclear whether bacterial physiology can affect RDOM production. In this study, we conducted a batch culture using the marine bacterial isolate Alteromonas macleodii, a ubiquitous gammaproteobacterium, to evaluate the linkage between bacterial growth and DOM production. Glucose (1 mmol C L-1) was used as the sole carbon source, and the bacterial number, the DOM concentration in terms of carbon, and the excitation–emission matrices (EEMs) of DOM were monitored during the 168-h incubation. The incubation period was partitioned into the exponential growth (0–24 h) and stationary phases (24–168 h) based on the growth curve. Although the DOM concentration decreased during the exponential growth phase due to glucose consumption, it remained stable during the stationary phase, corresponding to approximately 4% of the initial glucose in terms of carbon. Distinct fluorophores were not evident in the EEMs at the beginning of the incubation, but DOM produced by the strain exhibited five fluorescent peaks during exponential growth. Two fluorescent peaks were similar to protein-like fluorophores, while the others could be categorized as humic-like fluorophores. All fluorophores increased during the exponential growth phase. The tryptophan-like fluorophore decreased during the stationary phase, suggesting that the strain reused the large exopolymer. The tyrosine-like fluorophore seemed to be stable during the stationary phase, implying that the production of tyrosine-containing small peptides through the degradation of exopolymers was correlated with the reutilization of the tyrosine-like fluorophore. Two humic-like fluorophores that showed emission maxima at the longer wavelength (525 nm) increased during the stationary phase

Bacterial and primary production in the pelagic zone of the Kara Sea

NASA Astrophysics Data System (ADS)

Sazhin, A. F.; Romanova, N. D.; Mosharov, S. A.

2010-10-01

Data on the bacterial and primary production, which were obtained simultaneously for the same water samples, are presented for three regions of the Kara Sea. The samples were collected for the transect westwards of the Yamal Peninsula, along the St. Anna Trough, and the transect in Ob Bay. Direct counts of the DAPI-stained bacterial cells were performed. The bacterial production and grazing rates were determined using a direct method when metabolic inhibitors vancomycin and penicillin were added. The primary production rates were estimated using the 14C method. The average primary production was 112.6, 58.5, and 28.7 mg C m-2 day-1, and the bacterial production was 12.8, 48.9, and 81.6 mg C m-2 day-1 along the Yamal Peninsula, the St. Anna Trough, and Ob Bay, respectively. The average bacterial carbon demand was 34.6, 134.5, and 220.4 mg C m-2 day-1 for these regions, respectively. The data obtained lead us to conclude that the phytoplankton-synthesized organic matter is generally insufficient to satisfy the bacterial carbon demand and may be completely assimilated via the heterotrophic processes in the marine ecosystems. Therefore, the bacterial activity and, consequently, the amount of the synthesized biomass (i.e., the production) both depend directly on the phytoplankton’s condition and activity. We consider these relationships to be characteristics of the Kara Sea’s biota.

Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China.

PubMed

Guan, Xiangyu; Zhu, Lingling; Li, Youxun; Xie, Yuxuan; Zhao, Mingzhang; Luo, Ximing

2014-04-01

With rapid urbanization, anthropogenic activities are increasingly influencing the natural environment of the Bohai Bay. In this study, the composition and variation of bacterial and nirS-harboring bacterial communities in the coastal zone sediments of the Bohai Gulf were analyzed using PCR-based clone libraries. A total of 95 genera were detected in the bacterial communities, with Proteobacteria (72.1 %), Acidobacteria (10.5 %), Firmicutes (1.7 %), Bacteroidetes (1.4 %), Chloroflexi (0.7 %) and Planctomycetes (0.7 %) being the dominated phyla. The NirS sequences were divided into nine Clusters (A-I). Canonical correlation analysis showed that the bacterial or denitrifying communities were correlated with different environmental factors, such as total organic carbon, total nitrogen, ammonium, sulfate, etc. Furthermore, bacterial communities' composition and diversity are influenced by oil exploration, sewage discharge and other anthropogenic activities in the coastal area of the Bohai Sea. Thus, this study provided useful information on further research on regional or global environmental control and restore.

Nanoparticulate carbon black in cigarette smoke induces DNA cleavage and Th17-mediated emphysema.

PubMed

You, Ran; Lu, Wen; Shan, Ming; Berlin, Jacob M; Samuel, Errol Lg; Marcano, Daniela C; Sun, Zhengzong; Sikkema, William Ka; Yuan, Xiaoyi; Song, Lizhen; Hendrix, Amanda Y; Tour, James M; Corry, David B; Kheradmand, Farrah

2015-10-05

Chronic inhalation of cigarette smoke is the major cause of sterile inflammation and pulmonary emphysema. The effect of carbon black (CB), a universal constituent of smoke derived from the incomplete combustion of organic material, in smokers and non-smokers is less known. In this study, we show that insoluble nanoparticulate carbon black (nCB) accumulates in human myeloid dendritic cells (mDCs) from emphysematous lung and in CD11c(+) lung antigen presenting cells (APC) of mice exposed to smoke. Likewise, nCB intranasal administration induced emphysema in mouse lungs. Delivered by smoking or intranasally, nCB persisted indefinitely in mouse lung, activated lung APCs, and promoted T helper 17 cell differentiation through double-stranded DNA break (DSB) and ASC-mediated inflammasome assembly in phagocytes. Increasing the polarity or size of CB mitigated many adverse effects. Thus, nCB causes sterile inflammation, DSB, and emphysema and explains adverse health outcomes seen in smokers while implicating the dangers of nCB exposure in non-smokers.

Bacterial oxidation of dibromomethane and methyl bromide in natural waters and enrichment cultures

USGS Publications Warehouse

Goodwin, K.D.; Schaefer, J.K.; Oremland, R.S.

1998-01-01

Bacterial oxidation of 14CH2Br2 and 14CH3Br was measured in freshwater, estuarine, seawater, and hypersaline-alkaline samples. In general, bacteria from the various sites oxidized similar amounts of 14CH2Br2 and comparatively less 14CH3Br. Bacterial oxidation of 14CH3Br was rapid in freshwater samples compared to bacterial oxidation of 14CH3Br in more saline waters. Freshwater was also the only site in which methyl fluoride-sensitive bacteria (e.g., methanotrophs or nitrifiers) governed brominated methane oxidation. Half-life calculations indicated that bacterial oxidation of CH2Br2 was potentially significant in all of the waters tested. In contrast, only in freshwater was bacterial oxidation of CH3Br as fast as chemical removal. The values calculated for more saline sites suggested that bacterial oxidation of CH3Br was relatively slow compared to chemical and physical loss mechanisms. However, enrichment cultures demonstrated that bacteria in seawater can rapidly oxidize brominated methanes. Two distinct cultures of nonmethanotrophic methylotrophs were recovered; one of these cultures was able to utilize CH2Br2 as a sole carbon source, and the other was able to utilize CH3Br as a sole carbon source.

Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral Control?

PubMed Central

Rassner, Sara M. E.; Anesio, Alexandre M.; Girdwood, Susan E.; Hell, Katherina; Gokul, Jarishma K.; Whitworth, David E.; Edwards, Arwyn

2016-01-01

Glacial ice surfaces represent a seasonally evolving three-dimensional photic zone which accumulates microbial biomass and potentiates positive feedbacks in ice melt. Since viruses are abundant in glacial systems and may exert controls on supraglacial bacterial production, we examined whether changes in resource availability would promote changes in the bacterial community and the dynamics between viruses and bacteria of meltwater from the photic zone of a Svalbard glacier. Our results indicated that, under ambient nutrient conditions, low estimated viral decay rates account for a strong viral control of bacterial productivity, incurring a potent viral shunt of a third of bacterial carbon in the supraglacial microbial loop. Moreover, it appears that virus particles are very stable in supraglacial meltwater, raising the prospect that viruses liberated in melt are viable downstream. However, manipulating resource availability as dissolved organic carbon, nitrogen, and phosphorous in experimental microcosms demonstrates that the photic zone bacterial communities can escape viral control. This is evidenced by a marked decline in virus-to-bacterium ratio (VBR) concomitant with increased bacterial productivity and number. Pyrosequencing shows a few bacterial taxa, principally Janthinobacterium sp., dominate both the source meltwater and microcosm communities. Combined, our results suggest that viruses maintain high VBR to promote contact with low-density hosts, by the manufacture of robust particles, but that this necessitates a trade-off which limits viral production. Consequently, dominant bacterial taxa appear to access resources to evade viral control. We propose that a delicate interplay of bacterial and viral strategies affects biogeochemical cycling upon glaciers and, ultimately, downstream ecosystems. PMID:27446002

FT-Raman spectroscopic analysis of enhanced activity of supercritical carbon dioxide treated bacterial alpha-amylase.

PubMed

Paul, Kaninika; Dutta, Sayantani; Bhattacharjee, Paramita

2017-09-01

Our previous investigation on high pressure supercritical carbon dioxide treatment of a bacterial α-amylase had revealed enhanced activity of the same. 1 H NMR analysis of the activity enhanced enzyme led the authors to hypothesize that the enhancement was possibly owing to alterations in the active site of the enzyme. In the present study, the changes in the active site of the treated enzyme was analysed by Fourier-transform Raman (FT-Raman) spectroscopy. The spectra obtained revealed shifting of bands in the active site of α-amylase indicating a nudging effect of the bonds in this region consequent to high pressure treatment. Also, shifts in bands in the OH stretching vibration of water were observed in the enzyme spectra. These variations in the spectra confirmed changes in the active site as well as in the water associated with the same that perhaps had a concerted effect on the increased activity of α-amylase. Copyright © 2017 Elsevier Inc. All rights reserved.

Boosting current generation in microbial fuel cells by an order of magnitude by coating an ionic liquid polymer on carbon anodes.

PubMed

Yang, Lu; Deng, Wenfang; Zhang, Youming; Tan, Yueming; Ma, Ming; Xie, Qingji

2017-05-15

Microbial fuel cells (MFCs) have attracted great attentions due to their great application potentials, but the relatively low power densities of MFCs still hinder their widespread practical applications. Herein, we report that the current generation in MFCs can be boosted by an order of magnitude, simply by coating a hydrophilic and positively charged ionic liquid polymer (ILP) on carbon cloth (CC) or carbon felt (CF). The ILP coating not only can increase the bacterial loading capacity due to the electrostatic interactions between ILP and bacterial cells, but also can improve the mediated extracellular electron transfer between the electrode and the cytochrome proteins on the outer membrane of Shewanella putrefaciens cells. As a result, the maximum power density of a MFC equipped with the CF-ILP bioanode is as high as 4400±170mWm -2 , which is amongst the highest values reported to date. This work demonstrates a new strategy for greatly boosting the current generation in MFCs. Copyright © 2017 Elsevier B.V. All rights reserved.

All-solid-state flexible supercapacitors fabricated with bacterial nanocellulose papers, carbon nanotubes, and triblock-copolymer ion gels.

PubMed

Kang, Yu Jin; Chun, Sang-Jin; Lee, Sung-Suk; Kim, Bo-Yeong; Kim, Jung Hyeun; Chung, Haegeun; Lee, Sun-Young; Kim, Woong

2012-07-24

We demonstrate all-solid-state flexible supercapacitors with high physical flexibility, desirable electrochemical properties, and excellent mechanical integrity, which were realized by rationally exploiting unique properties of bacterial nanocellulose, carbon nanotubes, and ionic liquid based polymer gel electrolytes. This deliberate choice and design of main components led to excellent supercapacitor performance such as high tolerance against bending cycles and high capacitance retention over charge/discharge cycles. More specifically, the performance of our supercapacitors was highly retained through 200 bending cycles to a radius of 3 mm. In addition, the supercapacitors showed excellent cyclability with C(sp) (~20 mF/cm(2)) reduction of only <0.5% over 5000 charge/discharge cycles at the current density of 10 A/g. Our demonstration could be an important basis for material design and development of flexible supercapacitors.

The response of soil carbon storage and microbially mediated carbon turnover to simulated climatic disturbance in a northern peatland forest. Revisiting the concept of soil organic matter recalcitrance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostka, Joel

the chemical evolution of peat, with large shifts in microbial populations occurring in the biogeochemical hotspot, the mesotelm, where the highest rates of decomposition were detected. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens dominated in the deeper catotelm. Evidence pointed to the availability of phosphorus as well as nitrogen limiting the microbially-mediated turnover of organic carbon at MEF. Prior to initiation of the experimental treatments, our study provided key baseline data for the SPRUCE site on the vertical stratification of peat decomposition, key enzymatic pathways, and microbial taxa containing these pathways. The sensitivity of soil carbon turnover to climate change is strongly linked to recalcitrant carbon stocks and the temperature sensitivity of decomposition is thought to increase with increasing molecular complexity of carbon substrates. This project delivered results on how climate change perturbations impact the microbially-mediated turnover of recalcitrant organic matter in peatland forest soils, both under controlled conditions in the laboratory and at the ecosystem-scale in the field. This project revisited the concept of “recalcitrance” in the regulation of soil carbon turnover using a combination of natural abundance radiocarbon and optical spectroscopic measurements on bulk DOM, and high resolution molecular characterization of DOM. The project elucidated how organic matter reactivity and decomposition will respond to climate change in a both a qualitative (organic matter lability) and quantitiative (increased rates) manner. An Aromaticity Index was developed to represent a more direct and accurate parameter for modeling of DOM reactivity in peatlands. The abundance and community composition of soil

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships.

PubMed

Laforest-Lapointe, Isabelle; Paquette, Alain; Messier, Christian; Kembel, Steven W

2017-06-01

Research on biodiversity and ecosystem functioning has demonstrated links between plant diversity and ecosystem functions such as productivity. At other trophic levels, the plant microbiome has been shown to influence host plant fitness and function, and host-associated microbes have been proposed to influence ecosystem function through their role in defining the extended phenotype of host organisms However, the importance of the plant microbiome for ecosystem function has not been quantified in the context of the known importance of plant diversity and traits. Here, using a tree biodiversity-ecosystem functioning experiment, we provide strong support for the hypothesis that leaf bacterial diversity is positively linked to ecosystem productivity, even after accounting for the role of plant diversity. Our results also show that host species identity, functional identity and functional diversity are the main determinants of leaf bacterial community structure and diversity. Our study provides evidence of a positive correlation between plant-associated microbial diversity and terrestrial ecosystem productivity, and a new mechanism by which models of biodiversity-ecosystem functioning relationships can be improved.

Predominance of anaerobic bacterial community over aerobic community contribute to intensify ‘oxygen minimum zone’ in the eastern Arabian Sea

NASA Astrophysics Data System (ADS)

Gonsalves, M.-J.; Paropkari, A. L.; Fernandes, C. E. G.; Loka Bharathi, P. A.; Krishnakumari, L.; Fernando, V.; Nampoothiri, G. E.

2011-08-01

The presence of a delicately poised mid-depth oxygen minimum zone (OMZ) makes the Arabian Sea a unique and important ecosystem. So far, various aspects responsible for its formation have been studied. However, the contributions from bacterial groups mediating its formation and maintaining its intensity are described for the first time in this study. Thus, we hypothesize that the bacterial dynamics along with organic carbon loading result in bringing about differences in the intensity of OMZ between two stations in the Eastern Arabian Sea (EAS). Water column from 2 stations, one from offshore and another from slope, in the EAS were examined for phytoplankton diversity and pertinent groups of culturable bacteria. Vertical profiles of dissolved oxygen, productivity, chlorophyll a, total organic carbon and different physiological groups of bacteria showed well-defined stratified patterns in tandem with physical and chemical stratifications of the water column. The phytoplankton diversity was higher at the slope station (SS) and was dominated by the heterotrophic dinoflagellates. The offshore station (OS) on the other hand, showed lower diversity dominated by diatoms ( p<0.05). This observation could imply relatively higher autotrophy at the OS. Our results show that OMZ from these 'oligotrophic' regions is dominated by anaerobic bacteria. We believe that these bacteria contribute to intensify the OMZ in the EAS. Further, a higher abundance of viable anaerobic bacteria (TVC anaero) and other anaerobic groups at the SS than the OS suggest that the OMZ is relatively much more intense near the slope. Besides, total organic carbon (TOC) load is three-fold higher at the SS than at OS implying its higher accumulation and lower degradability in slope waters. Settling of this more preserved organic carbon in mid-slope sediments in contact with OMZ results in one of the highest enrichments of sedimentary TOC in the world oceans.

Dislocation-mediated growth of bacterial cell walls

PubMed Central

Amir, Ariel; Nelson, David R.

2012-01-01

Recent experiments have illuminated a remarkable growth mechanism of rod-shaped bacteria: proteins associated with cell wall extension move at constant velocity in circles oriented approximately along the cell circumference [Garner EC, et al., (2011) Science 333:222–225], [Domínguez-Escobar J, et al. (2011) Science 333:225–228], [van Teeffelen S, et al. (2011) PNAS 108:15822–15827]. We view these as dislocations in the partially ordered peptidoglycan structure, activated by glycan strand extension machinery, and study theoretically the dynamics of these interacting defects on the surface of a cylinder. Generation and motion of these interacting defects lead to surprising effects arising from the cylindrical geometry, with important implications for growth. We also discuss how long range elastic interactions and turgor pressure affect the dynamics of the fraction of actively moving dislocations in the bacterial cell wall. PMID:22660931

Near-infrared surface-enhanced-Raman-scattering (SERS) mediated identification of single optically trapped, bacterial spores

NASA Astrophysics Data System (ADS)

Alexander, Troy A.; Gillespie, James B.; Pellegrino, Paul M.; Fell, Nicholas F., Jr.; Wood, Gary L.; Salamo, Gregory J.

2003-03-01

A novel methodology has been developed for the investigation of bacterial spores. Specifically, this method has been used to probe the spore coat composition of several Bacillus species. This technique may be useful in many applications; most notably, development of novel detection schemes toward potentially harmful biological agents. This method would also be useful as an ancillary environmental monitoring system where sterility is of importance (i.e., food preparation areas as well as invasive and minimally invasive medical applications). This unique detection scheme is based on the near-infrared (NIR) Surface-Enhanced-Raman-Scattering (SERS) from single, optically trapped, bacterial spores. The SERS spectra of several bacterial spores in aqueous media have been measured using SERS substrates based on 60-nm diameter gold colloids bound to 3-Aminopropyltriethoxysilane derivatized glass. The light from a 785-nm laser diode was used to capture/manipulate as well as simultaneously excite the SERS of an individual bacterial spore. The collected SERS spectra were examined for uniqueness and the applicability of this technique for the species identification of bacterial spores.

Selective molecular transport through the protein shell of a bacterial microcompartment organelle

DOE PAGES

Chowdhury, Chiranjit; Chun, Sunny; Pang, Allan; ...

2015-02-23

Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions. In this paper, biochemical and physiological studies of structure-guided mutants are used to show that the hexameric PduA shell protein of the 1,2-propanediol utilization (Pdu) microcompartment forms a selectively permeable pore tailored for the influx of 1,2-propanediol (the substrate of the Pdu microcompartment) while restricting the efflux ofmore » propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism. Crystal structures of various PduA mutants provide a foundation for interpreting the observed biochemical and phenotypic data in terms of molecular diffusion across the shell. Finally and overall, these studies provide a basis for understanding a class of selectively permeable channels formed by nonmembrane proteins.« less

Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.

2011-04-18

Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeledmore » DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial

Sodium hydroxide-mediated hydrogel of citrus pectin for preparation of fluorescent carbon dots for bioimaging.

PubMed

Zhao, Xi Juan; Zhang, Wen Lin; Zhou, Zhi Qin

2014-11-01

The citrus process industry produces annually a huge amount of pomace, which is a rich source of citrus pectin. Here, we report the hydrogel of citrus pectin mediated by sodium hydroxide can be used to prepare fluorescent carbon dots (CDs). The introduction of hydrogel can not only make the temperature of the hydrothermal reaction down to 100 °C, but also avoid visually carbonized precipitates in the synthesis process even up to 180 °C. The as-synthesized CDs are well dispersed in water with an average size of 2.7 nm and show cyan fluorescence with high photostability, good biocompatibility. Furthermore, the CDs can act as a potential fluorescent probe for cell imaging. Citrus pectin as a non-toxic carbonaceous precursor for preparation of fluorescent CDs provides a new approach for the efficient utilization of citrus germplasm in future. Copyright © 2014 Elsevier B.V. All rights reserved.

Bacterial Communities in the Groundwater of Xikuangshan Antimony Mine, China

NASA Astrophysics Data System (ADS)

Wu, M.; Wang, H.; Wang, N.; Wang, M.

2017-12-01

Xikuangshan (XKS) is the biggest antimony (Sb) mine around the word, which causes serious environmental contamination due to the mining actives. To fully understand the bacterial compositions in the groundwater around the mining area in XKS and their correlation with environmental factors, groundwater samples were collected and subject to 16S rDNA high throughput sequencing. Results indicated that Proteobacteria (especially Gamma-Proteobacteria) dominated bacterial communities in high-Sb groundwater samples, whereas Bacteroidetes predominated in low-Sb groundwater. Furthermore, antimony concentration was found to be the most significant factor shaping bacterial communities (P=0.002) with an explanation of 9.16% of the variation. Other factors such as pH, contents of Mg, Ca and orthophosphate were also observed to significantly correlate with bacterial communities. This was the first report to show the important impact of Sb concentration on bacterial community structure in the groundwater in the mining area. Our results will enhance the understanding of subsurface biogeochemical processes mediated by microbes.

Uncoupling of Bacterial and Terrigenous Dissolved Organic Matter Dynamics in Decomposition Experiments

PubMed Central

Herlemann, Daniel P. R.; Manecki, Marcus; Meeske, Christian; Pollehne, Falk; Labrenz, Matthias; Schulz-Bull, Detlef; Dittmar, Thorsten; Jürgens, Klaus

2014-01-01

The biodegradability of terrigenous dissolved organic matter (tDOM) exported to the sea has a major impact on the global carbon cycle, but our understanding of tDOM bioavailability is fragmentary. In this study, the effects of preparative tDOM isolation on microbial decomposition were investigated in incubation experiments consisting of mesocosms containing mesohaline water from the Baltic Sea. Dissolved organic carbon (DOC) consumption, molecular DOM composition, bacterial activities, and shifts in bacterial community structure were compared between mesocosms supplemented with riverine tDOM, either as filtered, particle-free river water or as a concentrate obtained by lyophilization/tangential ultrafiltration, and those containing only Baltic Sea water or river water. As shown using ultra-high-resolution mass spectrometry (15 Tesla Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) covering approximately 4600 different DOM compounds, the three DOM preparation protocols resulted in distinct patterns of molecular DOM composition. However, despite DOC losses of 4–16% and considerable bacterial production, there was no significant change in DOM composition during the 28-day experiment. Moreover, tDOM addition affected neither DOC degradation nor bacterial dynamics significantly, regardless of the tDOM preparation. This result suggested that the introduced tDOM was largely not bioavailable, at least on the temporal scale of our experiment, and that the observed bacterial activity and DOC decomposition mainly reflected the degradation of unknown, labile, colloidal and low-molecular weight DOM, both of which escape the analytical window of FT-ICR-MS. In contrast to the different tDOM preparations, the initial bacterial inoculum and batch culture conditions determined bacterial community succession and superseded the effects of tDOM addition. The uncoupling of tDOM and bacterial dynamics suggests that mesohaline bacterial communities cannot

Malate-mediated carbon catabolite repression in Bacillus subtilis involves the HPrK/CcpA pathway.

PubMed

Meyer, Frederik M; Jules, Matthieu; Mehne, Felix M P; Le Coq, Dominique; Landmann, Jens J; Görke, Boris; Aymerich, Stéphane; Stülke, Jörg

2011-12-01

Most organisms can choose their preferred carbon source from a mixture of nutrients. This process is called carbon catabolite repression. The Gram-positive bacterium Bacillus subtilis uses glucose as the preferred source of carbon and energy. Glucose-mediated catabolite repression is caused by binding of the CcpA transcription factor to the promoter regions of catabolic operons. CcpA binds DNA upon interaction with its cofactors HPr(Ser-P) and Crh(Ser-P). The formation of the cofactors is catalyzed by the metabolite-activated HPr kinase/phosphorylase. Recently, it has been shown that malate is a second preferred carbon source for B. subtilis that also causes catabolite repression. In this work, we addressed the mechanism by which malate causes catabolite repression. Genetic analyses revealed that malate-dependent catabolite repression requires CcpA and its cofactors. Moreover, we demonstrate that HPr(Ser-P) is present in malate-grown cells and that CcpA and HPr interact in vivo in the presence of glucose or malate but not in the absence of a repressing carbon source. The formation of the cofactor HPr(Ser-P) could be attributed to the concentrations of ATP and fructose 1,6-bisphosphate in cells growing with malate. Both metabolites are available at concentrations that are sufficient to stimulate HPr kinase activity. The adaptation of cells to environmental changes requires dynamic metabolic and regulatory adjustments. The repression strength of target promoters was similar to that observed in steady-state growth conditions, although it took somewhat longer to reach the second steady-state of expression when cells were shifted to malate.

Down-regulation of monocarboxylate transporter 1 (MCT1) gene expression in the colon of piglets is linked to bacterial protein fermentation and pro-inflammatory cytokine-mediated signalling.

PubMed

Villodre Tudela, Carmen; Boudry, Christelle; Stumpff, Friederike; Aschenbach, Jörg R; Vahjen, Wilfried; Zentek, Jürgen; Pieper, Robert

2015-02-28

The present study investigated the influence of bacterial metabolites on monocarboxylate transporter 1 (MCT1) expression in pigs using in vivo, ex vivo and in vitro approaches. Piglets (n 24) were fed high-protein (26 %) or low-protein (18 %) diets with or without fermentable carbohydrates. Colonic digesta samples were analysed for a broad range of bacterial metabolites. The expression of MCT1, TNF-α, interferon γ (IFN-γ) and IL-8 was determined in colonic tissue. The expression of MCT1 was lower and of TNF-α and IL-8 was higher with high-protein diets (P< 0·05). MCT1 expression was positively correlated with l-lactate, whereas negatively correlated with NH₃ and putrescine (P< 0·05). The expression of IL-8 and TNF-α was negatively correlated with l-lactate and positively correlated with NH₃ and putrescine, whereas the expression of IFN-γ was positively correlated with histamine and 4-ethylphenol (P< 0·05). Subsequently, porcine colonic tissue and Caco-2 cells were incubated with Na-butyrate, NH₄Cl or TNF-α as selected bacterial metabolites or mediators of inflammation. Colonic MCT1 expression was higher after incubation with Na-butyrate (P< 0·05) and lower after incubation with NH₄Cl or TNF-α (P< 0·05). Incubation of Caco-2 cells with increasing concentrations of these metabolites confirmed the up-regulation of MCT1 expression by Na-butyrate (linear, P< 0·05) and down-regulation by TNF-α and NH₄Cl (linear, P< 0·05). The high-protein diet decreased the expression of MCT1 in the colon of pigs, which appears to be linked to NH₃- and TNF-α-mediated signalling.

Bacterially induced precipitation of CaCO sub 3 : An example from studies of cyanobacterial mats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chafetz, H.S.

1990-04-30

Bacteria induce the precipitation of calcium carbonate in the laboratory and in nature by altering their chemical environment. Geologists are recognizing the possibility that bacterially induced precipitates may form significant mineral deposits, unfortunately, there are currently no sound criteria by which they can be recognized in recent sediments, or in the rock record. Cultures of aerobic and facultative bacteria from cyanobacterial mats on Andros Island, Bahamas, and Baffin Bay, Texas, induced the precipitation of calcium carbonate under controlled conditions. Crusts, the largest features formed, are composed of 5--200{mu}m diameter bundles which are, in turn, composed of numerous individual crystals. Themore » smallest observed features are 0.1--0.4{mu}m spheres and rods which comprise some individual crystals and crystal bundles. Crystal bundles resembling rhombohedra, tetragonal disphenoids, tetragonal dipyramids, and calcite dumbbells appear to be uniquely bacterial in origin, and they have all been observed in recent sediments. Swollen rods, discs, curved dumbbells, and 50--200{mu}m optically continuous crystals resembling brushes may be uniquely bacterial in origin, however, they have not been reported by other laboratories nor observed in natural settings. Presence of any of these forms in recent sediments should be taken as strong evidence for bacterial influence. Spheres and aragonite dumbbells have also been observed in natural environments, however, they are not always bacterial in origin. Precipitation of calcium carbonate occurs preferentially on dead cyanobacteria in the presence of bacteria. Lithification of algal mats to form stromatolites may take place in the zone of decaying organic matter due to bacterial activity.« less

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios

PubMed Central

Eiler, Alexander; Biasi, Christina; Tuittila, Eeva-Stiina; Yrjälä, Kim; Fritze, Hannu

2016-01-01

ABSTRACT Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2. The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4. RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria. The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia. Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands. IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios.

PubMed

Juottonen, Heli; Eiler, Alexander; Biasi, Christina; Tuittila, Eeva-Stiina; Yrjälä, Kim; Fritze, Hannu

2017-02-15

Northern peatlands in general have high methane (CH 4 ) emissions, but individual peatlands show considerable variation as CH 4 sources. Particularly in nutrient-poor peatlands, CH 4 production can be low and exceeded by carbon dioxide (CO 2 ) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO 2 to CH 4 produced. After [ 13 C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH 4 and CO 2 The oligotrophic fen had lower CH 4 production but produced 3 to 59 times more CO 2 than CH 4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH 4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO 2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH 4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO 2 production in peatlands. Peatlands are major sources of the greenhouse gas methane (CH 4 ), yet in many peatlands, CO 2 production from unresolved anaerobic processes exceeds CH 4 production. Anaerobic

Variations in the patterns of soil organic carbon mineralization and microbial communities in response to exogenous application of rice straw and calcium carbonate.

PubMed

Feng, Shuzhen; Huang, Yuan; Ge, Yunhui; Su, Yirong; Xu, Xinwen; Wang, Yongdong; He, Xunyang

2016-11-15

The addition of exogenous inorganic carbon (CaCO3) and organic carbon has an important influence on soil organic carbon (SOC) mineralization in karst soil, but the microbial mechanisms underlying the SOC priming effect are poorly understood. We conducted a 100-day incubation experiment involving four treatments of the calcareous soil in southwestern China's karst region: control, (14)C-labeled rice straw addition, (14)C-labeled CaCO3 addition, and a combination of (14)C-labeled rice straw and CaCO3. Changes in soil microbial communities were characterized using denaturing gradient gel electrophoresis with polymerase chain reaction (PCR-DGGE) and real-time quantitative PCR (q-PCR). Both (14)C-rice straw and Ca(14)CO3 addition stimulated SOC mineralization, suggesting that organic and inorganic C affected SOC stability. Addition of straw alone had no significant effect on bacterial diversity; however, when the straw was added in combination with calcium carbonate, it had an inhibitory effect on bacterial and fungal diversity. At the beginning of the experimental period, exogenous additives increased bacterial abundance, although at the end of the 100-day incubation bacterial community abundance had gradually declined. Incubation time, exogenous input, and their interaction significantly affected SOC mineralization (in terms of priming and the cumulative amount of mineralization), microbial biomass carbon (MBC), and microbial community abundance and diversity. Moreover, the key factors influencing SOC mineralization were MBC, bacterial diversity, and soil pH. Overall, these findings support the view that inorganic C is involved in soil C turnover with the participation of soil microbial communities, promoting soil C cycling in the karst region. Copyright © 2016 Elsevier B.V. All rights reserved.

Transition metal ions mediated tyrosine based short peptide amphiphile nanostructures inhibit bacterial growth.

PubMed

Joshi, Khashti Ballabh; Singh, Ramesh; Mishra, Narendra Kumar; Kumar, Vikas; Vinayak, Vandana

2018-05-17

We report the design and synthesis of biocompatible small peptide based molecule for the controlled and targeted delivery of the encapsulated bioactive metal ions via transforming their internal nanostructures. Tyrosine based short peptide amphiphile (sPA) was synthesized which self-assembled into β-sheet like secondary structures. The self assembly of the designed sPA was modulated by using different bioactive transition metal ions which is confirmed by spectroscopic and microscopic techniques. These bioactive metal ions conjugated sPA hybrid structures are further used to develop antibacterial materials. It is due to the excellent antibacterial activity of zinc ions that the growth of clinically relevant bacteria such as E. Coli was inhibited in the presence of zinc-sPA conjugate. The bacterial test demonstrated that owing to high biocompatibility with bacterial cell, the designed sPA worked as metal ions delivery agent and therefore it can show great potential in locally addressing bacterial infections. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Influenza viral neuraminidase primes bacterial coinfection through TGF-β-mediated expression of host cell receptors.

PubMed

Li, Ning; Ren, Aihui; Wang, Xiaoshuang; Fan, Xin; Zhao, Yong; Gao, George F; Cleary, Patrick; Wang, Beinan

2015-01-06

Influenza infection predisposes the host to secondary bacterial pneumonia, which is a major cause of mortality during influenza epidemics. The molecular mechanisms underlying the bacterial coinfection remain elusive. Neuraminidase (NA) of influenza A virus (IAV) enhances bacterial adherence and also activates TGF-β. Because TGF-β can up-regulate host adhesion molecules such as fibronectin and integrins for bacterial binding, we hypothesized that activated TGF-β during IAV infection contributes to secondary bacterial infection by up-regulating these host adhesion molecules. Flow cytometric analyses of a human lung epithelial cell line indicated that the expression of fibronectin and α5 integrin was up-regulated after IAV infection or treatment with recombinant NA and was reversed through the inhibition of TGF-β signaling. IAV-promoted adherence of group A Streptococcus (GAS) and other coinfective pathogens that require fibronectin for binding was prevented significantly by the inhibition of TGF-β. However, IAV did not promote the adherence of Lactococcus lactis unless this bacterium expressed the fibronectin-binding protein of GAS. Mouse experiments showed that IAV infection enhanced GAS colonization in the lungs of wild-type animals but not in the lungs of mice deficient in TGF-β signaling. Taken together, these results reveal a previously unrecognized mechanism: IAV NA enhances the expression of cellular adhesins through the activation of TGF-β, leading to increased bacterial loading in the lungs. Our results suggest that TGF-β and cellular adhesins may be potential pharmaceutical targets for the prevention of coinfection.

Effects of Bacterial Microflora of the Lower Digestive Tract of Free-Range Waterfowl on Influenza Virus Activation ▿

PubMed Central

King, Marcus D.; Guentzel, M. Neal; Arulanandam, Bernard P.; Bodour, Adria A.; Brahmakshatriya, Vinayak; Lupiani, Blanca; Chambers, James P.

2011-01-01

Proteolytic cleavage activation of influenza virus hemagglutinin (HA0) is required for cell entry via receptor-mediated endocytosis. Despite numerous studies describing bacterial protease-mediated influenza A viral activation in mammals, very little is known about the role of intestinal bacterial flora of birds in hemagglutinin cleavage/activation. Therefore, the cloaca of wild waterfowl was examined for (i) representative bacterial types and (ii) their ability to cleave in a “trypsin-like” manner the precursor viral hemagglutinin molecule (HA0). Using radiolabeled HA0, bacterial secretion-mediated trypsin-like conversion of HA0 to HA1 and HA2 peptide products was observed to various degrees in 42 of 44 bacterial isolates suggestive of influenza virus activation in the cloaca of wild waterfowl. However, treatment of uncleaved virus with all bacterial isolates gave rise to substantially reduced emergent virus progeny compared with what was expected. Examination of two isolates exhibiting pronounced trypsin-like conversion of HA0 to HA1 and HA2 peptide products and low infectivity revealed lipase activity to be present. Because influenza virus possesses a complex lipid envelope, the presence of lipid hydrolase activity could in part account for the observed less-than-expected level of viable progeny. A thorough characterization of respective isolate protease HA0 hydrolysis products as well as other resident activities (i.e., lipase) is ongoing such that the role of these respective contributors in virus activation/inactivation can be firmly established. PMID:21531837

Linking Intertidal and Subtidal Food Webs: Consumer-Mediated Transport of Intertidal Benthic Microalgal Carbon

PubMed Central

Kang, Chang-Keun; Park, Hyun Je; Choy, Eun Jung; Choi, Kwang-Sik; Hwang, Kangseok; Kim, Jong-Bin

2015-01-01

We examined stable carbon and nitrogen isotope ratios for a large variety of consumers in intertidal and subtidal habitats, and their potential primary food sources [i.e., microphytobenthos (MPB), phytoplankton, and Phragmites australis] in a coastal bay system, Yeoja Bay of Korea, to test the hypothesis that the transfer of intertidal MPB-derived organic carbon to the subtidal food web can be mediated by motile consumers. Compared to a narrow δ13C range (−18 to −16‰) of offshore consumers, a broad δ13C range (−18 to −12‰) of both intertidal and subtidal consumers indicated that 13C-enriched sources of organic matter are an important trophic source to coastal consumers. In the intertidal areas, δ13C of most consumers overlapped with or was 13C-enriched relative to MPB. Despite the scarcity of MPB in the subtidal, highly motile consumers in subtidal habitat had nearly identical δ13C range with many intertidal foragers (including crustaceans and fish), overlapping with the range of MPB. In contrast, δ13C values of many sedentary benthic invertebrates in the subtidal areas were similar to those of offshore consumers and more 13C-depleted than motile foragers, indicating high dependence on phytoplankton-derived carbon. The isotopic mixing model calculation confirms that the majority of motile consumers and also some of subtidal sedentary ones depend on intertidal MPB for more than a half of their tissue carbon. Finally, although further quantitative estimates are needed, these results suggest that direct foraging by motile consumers on intertidal areas, and thereby biological transport of MPB-derived organic carbon to the subtidal areas, may provide important trophic connection between intertidal production and the nearshore shallow subtidal food webs. PMID:26448137

Through the eye of the needle: a review of isotope approaches to quantify microbial processes mediating soil carbon balance.

PubMed

Paterson, Eric; Midwood, Andrew J; Millard, Peter

2009-01-01

For soils in carbon balance, losses of soil carbon from biological activity are balanced by organic inputs from vegetation. Perturbations, such as climate or land use change, have the potential to disrupt this balance and alter soil-atmosphere carbon exchanges. As the quantification of soil organic matter stocks is an insensitive means of detecting changes, certainly over short timescales, there is a need to apply methods that facilitate a quantitative understanding of the biological processes underlying soil carbon balance. We outline the processes by which plant carbon enters the soil and critically evaluate isotopic methods to quantify them. Then, we consider the balancing CO(2) flux from soil and detail the importance of partitioning the sources of this flux into those from recent plant assimilate and those from native soil organic matter. Finally, we consider the interactions between the inputs of carbon to soil and the losses from soil mediated by biological activity. We emphasize the key functional role of the microbiota in the concurrent processing of carbon from recent plant inputs and native soil organic matter. We conclude that quantitative isotope labelling and partitioning methods, coupled to those for the quantification of microbial community substrate use, offer the potential to resolve the functioning of the microbial control point of soil carbon balance in unprecedented detail.

Plasmid-Mediated Bioaugmentation for the Bioremediation of Contaminated Soils

PubMed Central

Garbisu, Carlos; Garaiyurrebaso, Olatz; Epelde, Lur; Grohmann, Elisabeth; Alkorta, Itziar

2017-01-01

Bioaugmentation, or the inoculation of microorganisms (e.g., bacteria harboring the required catabolic genes) into soil to enhance the rate of contaminant degradation, has great potential for the bioremediation of soils contaminated with organic compounds. Regrettably, cell bioaugmentation frequently turns into an unsuccessful initiative, owing to the rapid decrease of bacterial viability and abundance after inoculation, as well as the limited dispersal of the inoculated bacteria in the soil matrix. Genes that encode the degradation of organic compounds are often located on plasmids and, consequently, they can be spread by horizontal gene transfer into well-established, ecologically competitive, indigenous bacterial populations. Plasmid-mediated bioaugmentation aims to stimulate the spread of contaminant degradation genes among indigenous soil bacteria by the introduction of plasmids, located in donor cells, harboring such genes. But the acquisition of plasmids by recipient cells can affect the host’s fitness, a crucial aspect for the success of plasmid-mediated bioaugmentation. Besides, environmental factors (e.g., soil moisture, temperature, organic matter content) can play important roles for the transfer efficiency of catabolic plasmids, the expression of horizontally acquired genes and, finally, the contaminant degradation activity. For plasmid-mediated bioaugmentation to be reproducible, much more research is needed for a better selection of donor bacterial strains and accompanying plasmids, together with an in-depth understanding of indigenous soil bacterial populations and the environmental conditions that affect plasmid acquisition and the expression and functioning of the catabolic genes of interest. PMID:29062312

Contribution of bacterial cells to lacustrine organic matter based on amino sugars and D-amino acids

NASA Astrophysics Data System (ADS)

Carstens, Dörte; Köllner, Krista E.; Bürgmann, Helmut; Wehrli, Bernhard; Schubert, Carsten J.

2012-07-01

Amino sugars (ASs), D-amino acids (D-AAs), and bacterial cell counts were measured in two Swiss lakes to study the contribution of bacterial cells to organic matter (OM) and the fate of ASs and bacterial amino biomarkers during OM degradation. Concentrations of individual ASs (glucosamine, galactosamine, muramic acid, and mannosamine) in the particulate and total OM pools were analyzed in water-column profiles of Lake Brienz (oligotrophic and oxic throughout the entire water column) and Lake Zug (eutrophic, stratified, and permanently anoxic below 170 m) in spring and in fall. Generally, carbon-normalized AS concentrations decreased with water depth, indicating the preferential decomposition of ASs. For Lake Brienz the relative loss of particulate ASs was higher than in Lake Zug, suggesting enhanced AS turnover in an oligotrophic environment. AS ratio changes in the water column revealed a replacement of plankton biomass with OM from heterotrophic microorganisms with increasing water depth. Similar to the ASs, highest carbon normalized D-AA concentrations were found in the upper water column with decreasing concentrations with depth and an increase close to the sediments. In Lake Zug, an increase in the percentage of D-AAs also showed the involvement of bacteria in OM degradation. Estimations of OM derived from bacterial cells using cell counts and the bacterial biomarkers muramic acid and D-AAs gave similar results. For Lake Brienz 0.2-14% of the organic carbon pool originated from bacterial cells, compared to only 0.1-5% in Lake Zug. Based on our estimates, muramic acid appeared primarily associated with bacterial biomass and not with refractory bacterial necromass. Our study underscores that bacteria are not only important drivers of OM degradation in lacustrine systems, they also represent a significant source of OM themselves, especially in oligotrophic lakes.

A microfluidic study of liquid-liquid extraction mediated by carbon dioxide.

PubMed

Lestari, Gabriella; Salari, Alinaghi; Abolhasani, Milad; Kumacheva, Eugenia

2016-07-05

Liquid-liquid extraction is an important separation and purification method; however, it faces a challenge in reducing the energy consumption and the environmental impact of solvent (extractant) recovery. The reversible chemical reactions of switchable solvents (nitrogenous bases) with carbon dioxide (CO2) can be implemented in reactive liquid-liquid extraction to significantly reduce the cost and energy requirements of solvent recovery. The development of new effective switchable solvents reacting with CO2 and the optimization of extraction conditions rely on the ability to evaluate and screen the performance of switchable solvents in extraction processes. We report a microfluidic strategy for time- and labour-efficient studies of CO2-mediated solvent extraction. The platform utilizes a liquid segment containing an aqueous extractant droplet and a droplet of a solution of a switchable solvent in a non-polar liquid, with gaseous CO2 supplied to the segment from both sides. Following the reaction of the switchable solvent with CO2, the solvent becomes hydrophilic and transfers from the non-polar solvent to the aqueous droplet. By monitoring the time-dependent variation in droplet volumes, we determined the efficiency and extraction time for the CO2-mediated extraction of different nitrogenous bases in a broad experimental parameter space. The platform enables a significant reduction in the amount of switchable solvents used in these studies, provides accurate temporal characterization of the liquid-liquid extraction process, and offers the capability of high-throughput screening of switchable solvents.

Metamorphosis of a butterfly-associated bacterial community.

PubMed

Hammer, Tobin J; McMillan, W Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

Metamorphosis of a Butterfly-Associated Bacterial Community

PubMed Central

Hammer, Tobin J.; McMillan, W. Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies. PMID:24466308

Composition and stability of bacterial communities associated with granular activated carbon and anthracite filters in a pilot scale municipal drinking water treatment facility.

PubMed

Shirey, T B; Thacker, R W; Olson, J B

2012-06-01

Granular activated carbon (GAC) is an alternative filter substrate for municipal water treatment as it provides a high surface area suitable for microbial colonization. The resulting microbial growth promotes biodegradation of organic materials and other contaminants from influent waters. Here, the community structure of the bacteria associated with three GAC and two anthracite filters was examined over 12 months to monitor changes in community composition. Nearly complete 16S rRNA genes were polymerase chain reaction amplified for terminal restriction fragment length polymorphism (T-RFLP) analyses. The identity of commonly occurring peaks was determined through the construction of five representative 16S rRNA clone libraries. Based on sequence analysis, the bacterial communities associated with both anthracite and GAC filters appear to be composed of environmentally derived bacteria, with no known human pathogens. Analysis of similarity tests revealed that significant differences in bacterial community structure occurred over time, with filter substrate playing an important role in determining community composition. GAC filters exhibited the greatest degree of bacterial community variability over the sampling period, while anthracite filters showed a lower degree of variability and less change in community composition. Thus, GAC may be a suitable biologically active filter substrate for the treatment of municipal drinking water.

Iron-mediated stabilization of soil carbon amplifies the benefits of ecological restoration in degraded lands.

PubMed

Silva, Lucas C R; Doane, Timothy A; Corrêa, Rodrigo S; Valverde, Vinicius; Pereira, Engil I P; Horwath, William R

2015-07-01

unsuccessful attempts to restore mined areas through nutrient application alone, iron-mediated stabilization of vegetation inputs favored the regeneration of a barren stable state that had persisted for over five decades since disturbance. The effectiveness of coupled organic matter and iron "fertilization," combined with management of invasive species, has the possibility to enhance terrestrial carbon sequestration and accelerate the restoration of degraded lands, while addressing important challenges associated with urban waste disposal.

Role of vegetation and edaphic factors in controlling diversity and use of different carbon sources in semi-arid ecosystems

NASA Astrophysics Data System (ADS)

Lohse, K. A.; McLain, J. E.; Harman, C. J.; Sivapalan, M.; Troch, P. A.

2010-12-01

Microbially-mediated soil carbon cycling is closely linked to soil moisture and temperature. Climate change is predicted to increase intra-annual precipitation variability (i.e. less frequent yet more intense precipitation events) and alter biogeochemical processes due to shifts in soil moisture dynamics and inputs of carbon. However, the responses of soil biology and chemistry to predicted climate change, and their concomitant feedbacks on ecosystem productivity and biogeochemical processes are poorly understood. We collected soils at three different elevations in the Santa Catalina Mountains, AZ and quantified carbon utilization during pre-monsoon precipitation conditions. Contrasting parent materials (schist and granite) were paired at each elevation. We expected climate to determine the overall activity of soil fungal and bacterial communities and diversity of soil C utilization, and differences in parent material to modify these responses through controls on soil physical properties. We used EcoPlateTM C utilization assays to determine the relative abundance of soil bacterial and fungal populations and rate and diversity of carbon utilization. Additional plates were incubated with inhibitors selective to fungal or bacterial activity to assess relative contribution of these microbial groups to overall C utilization. We analyzed soils for soil organic matter, total C and N, particle size analysis and soil moisture content via both gravimetric and volumetric methods to assess the influences of soil physical and chemical properties on the measured biological responses. Consistent with our expectations, overall microbial activity was highest at the uppermost conifer elevation sites compared to the middle and lower elevation sites. In contrast to our expectations, however, overall activity was lower at the mid elevation oak woodland sites compared to the low elevation desert sites. Also consistent with our expectations was the observation that overall activities

Determinants of bacterial communities in Canadian agroforestry systems.

PubMed

Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

2016-06-01

Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

CHANGES IN BACTERIAL COMPOSITION OF BIOFILM IN A ...

EPA Pesticide Factsheets

This study examined the development of bacterial biofilms within a metropolitan distribution system. The distribution system is fed with different source water (i.e., groundwater, GW and surface water, SW) and undergoes different treatment processes in separate facilities. The biofilm community was characterized using 16S rRNA gene clone libraries and functional potential analysis, generated from total DNA extracted from coupons in biofilm annular reactors fed with onsite drinking water for up to eighteen months. Significant differences in the bacterial community structure were observed between GW and SW. Representatives that explained the dissimilarity between service areas were associated with Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Gammaproteobacteria, and Firmicutes. After nine months the biofilm bacterial community from both areas were dominated by Mycobacterium species. The distribution of the dominant OTU (Mycobacterium) positively correlated with the drinking water distribution system (DWDS) temperature, but no clear relationship was seen with free chlorine residual, pH, turbidity or total organic carbon (TOC). The results suggest that biofilm microbial communities harbor distinct and diverse bacterial communities, and that source water, treatment processes and environmental conditions may play an important role in shaping the bacterial community in the distribution system. On the other hand, several bacterial groups were present i

Bithionol blocks pathogenicity of bacterial toxins, ricin, and Zika virus

USDA-ARS?s Scientific Manuscript database

Disease pathways form overlapping networks, and hub proteins represent attractive targets for broad-spectrum drugs. Using bacterial toxins as a proof of concept, we describe a new approach of discovering broad-spectrum therapies capable of inhibiting host proteins that mediate multiple pathogenic pa...

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps

PubMed Central

Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E.; Adatte, Thierry; Guisan, Antoine; van der Meer, Jan Roelof

2016-01-01

ABSTRACT Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. IMPORTANCE This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps.

PubMed

Yashiro, Erika; Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E; Adatte, Thierry; Niculita-Hirzel, Hélène; Guisan, Antoine; van der Meer, Jan Roelof

2016-11-01

Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km 2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700

Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations.

PubMed

Ghosh, Anirban; Baltekin, Özden; Wäneskog, Marcus; Elkhalifa, Dina; Hammarlöf, Disa L; Elf, Johan; Koskiniemi, Sanna

2018-05-02

Bacterial populations can use bet-hedging strategies to cope with rapidly changing environments. One example is non-growing cells in clonal bacterial populations that are able to persist antibiotic treatment. Previous studies suggest that persisters arise in bacterial populations either stochastically through variation in levels of global signalling molecules between individual cells, or in response to various stresses. Here, we show that toxins used in contact-dependent growth inhibition (CDI) create persisters upon direct contact with cells lacking sufficient levels of CdiI immunity protein, which would otherwise bind to and neutralize toxin activity. CDI-mediated persisters form through a feedforward cycle where the toxic activity of the CdiA toxin increases cellular (p)ppGpp levels, which results in Lon-mediated degradation of the immunity protein and more free toxin. Thus, CDI systems mediate a population density-dependent bet-hedging strategy, where the fraction of non-growing cells is increased only when there are many cells of the same genotype. This may be one of the mechanisms of how CDI systems increase the fitness of their hosts. © 2018 The Authors.

Nanoparticulate carbon black in cigarette smoke induces DNA cleavage and Th17-mediated emphysema

PubMed Central

You, Ran; Lu, Wen; Shan, Ming; Berlin, Jacob M; Samuel, Errol LG; Marcano, Daniela C; Sun, Zhengzong; Sikkema, William KA; Yuan, Xiaoyi; Song, Lizhen; Hendrix, Amanda Y; Tour, James M; Corry, David B; Kheradmand, Farrah

2015-01-01

Chronic inhalation of cigarette smoke is the major cause of sterile inflammation and pulmonary emphysema. The effect of carbon black (CB), a universal constituent of smoke derived from the incomplete combustion of organic material, in smokers and non-smokers is less known. In this study, we show that insoluble nanoparticulate carbon black (nCB) accumulates in human myeloid dendritic cells (mDCs) from emphysematous lung and in CD11c+ lung antigen presenting cells (APC) of mice exposed to smoke. Likewise, nCB intranasal administration induced emphysema in mouse lungs. Delivered by smoking or intranasally, nCB persisted indefinitely in mouse lung, activated lung APCs, and promoted T helper 17 cell differentiation through double-stranded DNA break (DSB) and ASC-mediated inflammasome assembly in phagocytes. Increasing the polarity or size of CB mitigated many adverse effects. Thus, nCB causes sterile inflammation, DSB, and emphysema and explains adverse health outcomes seen in smokers while implicating the dangers of nCB exposure in non-smokers. DOI: http://dx.doi.org/10.7554/eLife.09623.001 PMID:26437452

Reprogramming the Host Response in Bacterial Meningitis: How Best To Improve Outcome?

PubMed Central

van der Flier, M.; Geelen, S. P. M.; Kimpen, J. L. L.; Hoepelman, I. M.; Tuomanen, E. I.

2003-01-01

Despite effective antibiotic therapy, bacterial meningitis is still associated with high morbidity and mortality in both children and adults. Animal studies have shown that the host inflammatory response induced by bacterial products in the subarachnoid space is associated with central nervous system injury. Thus, attenuation of inflammation early in the disease process might improve the outcome. The feasibility of such an approach is demonstrated by the reduction in neurologic sequelae achieved with adjuvant dexamethasone therapy. Increased understanding of the pathways of inflammation and neuronal damage has suggested rational new targets to modulate the host response in bacterial meningitis, but prediction of which agents would be optimal has been difficult. This review compares the future promise of benefit from the use of diverse adjuvant agents. It appears unlikely that inhibition of a single proinflammatory mediator will prove useful in clinical practice, but several avenues to reprogram a wider array of mediators simultaneously are encouraging. Particularly promising are efforts to adjust combinations of cytokines, to inhibit neuronal apoptosis and to enhance brain repair. PMID:12857775

Impact of the 3 °C temperature rise on bacterial growth and carbon transfer towards higher trophic levels: Empirical models for the Adriatic Sea

NASA Astrophysics Data System (ADS)

Šolić, Mladen; Krstulović, Nada; Šantić, Danijela; Šestanović, Stefanija; Kušpilić, Grozdan; Bojanić, Natalia; Ordulj, Marin; Jozić, Slaven; Vrdoljak, Ana

2017-09-01

The Mediterranean Sea (including the Adriatic Sea) has been identified as a 'hotspot' for climate change, with the prediction of the increase in water temperature of 2-4 °C over the next few decades. Being mainly oligotrophic, and strongly phosphorus limited, the Adriatic Sea is characterized by the important role of the microbial food web in production and transfer of biomass and energy towards higher trophic levels. We hypothesized that predicted 3 °C temperature rise in the near future might cause an increase of bacterial production and bacterial losses to grazers, which could significantly enlarge the trophic base for metazoans. This empirical study is based on a combined 'space-for-time substitution' analysis (which is performed on 3583 data sets) and on an experimental approach (36 in situ grazing experiments performed at different temperatures). It showed that the predicted 3 °C temperature increase (which is a result of global warming) in the near future could cause a significant increase in bacterial growth at temperatures lower than 16 °C (during the colder winter-spring period, as well as in the deeper layers). The effect of temperature on bacterial growth could be additionally doubled in conditions without phosphorus limitation. Furthermore, a 3 °C increase in temperature could double the grazing on bacteria by heterotrophic nanoflagellate (HNF) and ciliate predators and it could increase the proportion of bacterial production transferred to the metazoan food web by 42%. Therefore, it is expected that global warming may further strengthen the role of the microbial food web in a carbon cycle in the Adriatic Sea.

Spatio-temporal patterns of major bacterial groups in alpine waters.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2014-01-01

Glacial alpine landscapes are undergoing rapid transformation due to changes in climate. The loss of glacial ice mass has directly influenced hydrologic characteristics of alpine floodplains. Consequently, hyporheic sediment conditions are likely to change in the future as surface waters fed by glacial water (kryal) become groundwater dominated (krenal). Such environmental shifts may subsequently change bacterial community structure and thus potential ecosystem functioning. We quantitatively investigated the structure of major bacterial groups in glacial and groundwater-fed streams in three alpine floodplains during different hydrologic periods. Our results show the importance of several physico-chemical variables that reflect local geological characteristics as well as water source in structuring bacterial groups. For instance, Alpha-, Betaproteobacteria and Cytophaga-Flavobacteria were influenced by pH, conductivity and temperature as well as by inorganic and organic carbon compounds, whereas phosphorous compounds and nitrate showed specific influence on single bacterial groups. These results can be used to predict future bacterial group shifts, and potential ecosystem functioning, in alpine landscapes under environmental transformation.

Camphor-mediated synthesis of carbon nanoparticles, graphitic shell encapsulated carbon nanocubes and carbon dots for bioimaging

PubMed Central

Oza, Goldie; Ravichandran, M.; Merupo, Victor-Ishrayelu; Shinde, Sachin; Mewada, Ashmi; Ramirez, Jose Tapia; Velumani, S.; Sharon, Madhuri; Sharon, Maheshwar

2016-01-01

A green method for an efficient synthesis of water-soluble carbon nanoparticles (CNPs), graphitic shell encapsulated carbon nanocubes (CNCs), Carbon dots (CDs) using Camphor (Cinnamomum camphora) is demonstrated. Here, we describe a competent molecular fusion and fission route for step-wise synthesis of CDs. Camphor on acidification and carbonization forms CNPs, which on alkaline hydrolysis form CNCs that are encapsulated by thick graphitic layers and on further reduction by sodium borohydride yielded CDs. Though excitation wavelength dependent photoluminescence is observed in all the three carbon nanostructures, CDs possess enhanced photoluminescent properties due to more defective carbonaceous structures. The surface hydroxyl and carboxyl functional groups make them water soluble in nature. They possess excellent photostability, higher quantum yield, increased absorption, decreased cytotoxicity and hence can be utilized as a proficient bio imaging agent. PMID:26905737

Camphor-mediated synthesis of carbon nanoparticles, graphitic shell encapsulated carbon nanocubes and carbon dots for bioimaging

NASA Astrophysics Data System (ADS)

Oza, Goldie; Ravichandran, M.; Merupo, Victor-Ishrayelu; Shinde, Sachin; Mewada, Ashmi; Ramirez, Jose Tapia; Velumani, S.; Sharon, Madhuri; Sharon, Maheshwar

2016-02-01

A green method for an efficient synthesis of water-soluble carbon nanoparticles (CNPs), graphitic shell encapsulated carbon nanocubes (CNCs), Carbon dots (CDs) using Camphor (Cinnamomum camphora) is demonstrated. Here, we describe a competent molecular fusion and fission route for step-wise synthesis of CDs. Camphor on acidification and carbonization forms CNPs, which on alkaline hydrolysis form CNCs that are encapsulated by thick graphitic layers and on further reduction by sodium borohydride yielded CDs. Though excitation wavelength dependent photoluminescence is observed in all the three carbon nanostructures, CDs possess enhanced photoluminescent properties due to more defective carbonaceous structures. The surface hydroxyl and carboxyl functional groups make them water soluble in nature. They possess excellent photostability, higher quantum yield, increased absorption, decreased cytotoxicity and hence can be utilized as a proficient bio imaging agent.

Controlled Zn-mediated grafting of thin layers of bipodal diazonium salt on gold and carbon substrates.

PubMed

Torréns, Mabel; Ortiz, Mayreli; Turner, Anthony P F; Beni, Valerio; O'Sullivan, Ciara K

2015-01-07

A controlled, rapid, and potentiostat-free method has been developed for grafting the diazonium salt (3,5-bis(4-diazophenoxy)benzoic acid tetrafluoroborate (DCOOH)) on gold and carbon substrates, based on a Zn-mediated chemical dediazonation. The highly stable thin layer organic platforms obtained were characterized by cyclic voltammetry, AFM, impedance, XP, and Raman spectroscopies. A dediazonation mechanism based on radical formation is proposed. Finally, DCOOH was proved as a linker to an aminated electroactive probe. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Folate receptor-mediated boron-10 containing carbon nanoparticles as potential delivery vehicles for boron neutron capture therapy of nonfunctional pituitary adenomas.

PubMed

Dai, Congxin; Cai, Feng; Hwang, Kuo Chu; Zhou, Yongmao; Zhang, Zizhu; Liu, Xiaohai; Ma, Sihai; Yang, Yakun; Yao, Yong; Feng, Ming; Bao, Xinjie; Li, Guilin; Wei, Junji; Jiao, Yonghui; Wei, Zhenqing; Ma, Wenbin; Wang, Renzhi

2013-02-01

Invasive nonfunctional pituitary adenomas (NFPAs) are difficult to completely resect and often develop tumor recurrence after initial surgery. Currently, no medications are clinically effective in the control of NFPA. Although radiation therapy and radiosurgery are useful to prevent tumor regrowth, they are frequently withheld because of severe complications. Boron neutron capture therapy (BNCT) is a binary radiotherapy that selectively and maximally damages tumor cells without harming the surrounding normal tissue. Folate receptor (FR)-targeted boron-10 containing carbon nanoparticles is a novel boron delivery agent that can be selectively taken up by FR-expressing cells via FR-mediated endocytosis. In this study, FR-targeted boron-10 containing carbon nanoparticles were selectively taken up by NFPAs cells expressing FR but not other types of non-FR expressing pituitary adenomas. After incubation with boron-10 containing carbon nanoparticles and following irradiation with thermal neutrons, the cell viability of NFPAs was significantly decreased, while apoptotic cells were simultaneously increased. However, cells administered the same dose of FR-targeted boron-10 containing carbon nanoparticles without neutron irradiation or received the same neutron irradiation alone did not show significant decrease in cell viability or increase in apoptotic cells. The expression of Bcl-2 was down-regulated and the expression of Bax was up-regulated in NFPAs after treatment with FR-mediated BNCT. In conclusion, FR-targeted boron-10 containing carbon nanoparticles may be an ideal delivery system of boron to NFPAs cells for BNCT. Furthermore, our study also provides a novel insight into therapeutic strategies for invasive NFPA refractory to conventional therapy, while exploring these new applications of BNCT for tumors, especially benign tumors.

Exploring bacterial lignin degradation.

PubMed

Brown, Margaret E; Chang, Michelle C Y

2014-04-01

Plant biomass represents a renewable carbon feedstock that could potentially be used to replace a significant level of petroleum-derived chemicals. One major challenge in its utilization is that the majority of this carbon is trapped in the recalcitrant structural polymers of the plant cell wall. Deconstruction of lignin is a key step in the processing of biomass to useful monomers but remains challenging. Microbial systems can provide molecular information on lignin depolymerization as they have evolved to break lignin down using metalloenzyme-dependent radical pathways. Both fungi and bacteria have been observed to metabolize lignin; however, their differential reactivity with this substrate indicates that they may utilize different chemical strategies for its breakdown. This review will discuss recent advances in studying bacterial lignin degradation as an approach to exploring greater diversity in the environment. Copyright © 2013 Elsevier Ltd. All rights reserved.

Acid Chlorides as Formal Carbon Dianion Linchpin Reagents in the Aluminum Chloride-Mediated Dieckmann Cyclization of Dicarboxylic Acids.

PubMed

Armaly, Ahlam M; Bar, Sukanta; Schindler, Corinna S

2017-08-04

The development of acid chlorides as formal dianion linchpin reagents that enable access to cyclic 2-alkyl- and 2-acyl-1,3-alkanediones from dicarboxylic acids is described herein. Mechanistic experiments relying on 13 C-labeling studies confirm the role of acid chlorides as carbon dianion linchpin reagents and have led to a revised reaction mechanism for the aluminum(III)-mediated Dieckmann cyclization of dicarboxylic acids with acid chlorides.

Bacterially induced precipitation of CaCO 3: An example from studies of cyanobacterial mats. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chafetz, Henry S.

1990-04-30

Bacteria induce the precipitation of calcium carbonate in the laboratory and in nature by altering their chemical environment. Geologists are recognizing the possibility that bacterially induced precipitates may form significant mineral deposits, unfortunately, there are currently no sound criteria by which they can be recognized in recent sediments, or in the rock record. Cultures of aerobic and facultative bacteria from cyanobacterial mats on Andros Island, Bahamas, and Baffin Bay, Texas, induced the precipitation of calcium carbonate under controlled conditions. Crusts, the largest features formed, are composed of 5--200μm diameter bundles which are, in turn, composed of numerous individual crystals. Themore » smallest observed features are 0.1--0.4μm spheres and rods which comprise some individual crystals and crystal bundles. Crystal bundles resembling rhombohedra, tetragonal disphenoids, tetragonal dipyramids, and calcite dumbbells appear to be uniquely bacterial in origin, and they have all been observed in recent sediments. Swollen rods, discs, curved dumbbells, and 50--200μm optically continuous crystals resembling brushes may be uniquely bacterial in origin, however, they have not been reported by other laboratories nor observed in natural settings. Presence of any of these forms in recent sediments should be taken as strong evidence for bacterial influence. Spheres and aragonite dumbbells have also been observed in natural environments, however, they are not always bacterial in origin. Precipitation of calcium carbonate occurs preferentially on dead cyanobacteria in the presence of bacteria. Lithification of algal mats to form stromatolites may take place in the zone of decaying organic matter due to bacterial activity.« less

Cloning and expression of gamma carbonic anhydrase from Serratia sp. ISTD04 for sequestration of carbon dioxide and formation of calcite.

PubMed

Srivastava, Shaili; Bharti, Randhir Kumar; Verma, Praveen Kumar; Thakur, Indu Shekhar

2015-01-01

Bacterial strains isolated from marble mines rock and enriched in the chemostat culture with different concentrations of sodium bicarbonate. The enriched consortium had six bacterial isolates. One of bacterium isolate showed carbonic anhydrase (CA) activity by catalyzing the reversible hydration reaction of carbon dioxide to bicarbonate. The bacterium was identified as Serratia sp. by 16S rRNA sequence analysis. The carbonic anhydrase gene from Serratia sp. was found to be homologous with gamma carbonic anhydrase. The carbonic anhydrase gene was cloned in PET21b(+) and expressed it in recombinant Escherichia coli BL21 (DE3) with His-tag at the C-terminus. The recombinant protein was purified efficiently by using one-step nickel affinity chromatography. Expected size of carbonic anhydrase was approximately 29 kDa in SDS-PAGE gel. Recombinant carbonic anhydrase enzyme was used for biomineralization-based conversion of atmospheric CO2 into valuable calcite minerals. The calcification was confirmed by using XRD, FTIR, EDX and SEM analysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Anti-Pseudomonas aeruginosa IgY Antibodies Induce Specific Bacterial Aggregation and Internalization in Human Polymorphonuclear Neutrophils

PubMed Central

Thomsen, K.; Christophersen, L.; Bjarnsholt, T.; Jensen, P. Ø.; Moser, C.

2015-01-01

Polymorphonuclear neutrophils (PMNs) are essential cellular constituents in the innate host response, and their recruitment to the lungs and subsequent ubiquitous phagocytosis controls primary respiratory infection. Cystic fibrosis pulmonary disease is characterized by progressive pulmonary decline governed by a persistent, exaggerated inflammatory response dominated by PMNs. The principal contributor is chronic Pseudomonas aeruginosa biofilm infection, which attracts and activates PMNs and thereby is responsible for the continuing inflammation. Strategies to prevent initial airway colonization with P. aeruginosa by augmenting the phagocytic competence of PMNs may postpone the deteriorating chronic biofilm infection. Anti-P. aeruginosa IgY antibodies significantly increase the PMN-mediated respiratory burst and subsequent bacterial killing of P. aeruginosa in vitro. The mode of action is attributed to IgY-facilitated formation of immobilized bacteria in aggregates, as visualized by fluorescence microscopy and the induction of increased bacterial hydrophobicity. Thus, the present study demonstrates that avian egg yolk immunoglobulins (IgY) targeting P. aeruginosa modify bacterial fitness, which enhances bacterial killing by PMN-mediated phagocytosis and thereby may facilitate a rapid bacterial clearance in airways of people with cystic fibrosis. PMID:25895968

The linkage between nutrient supply, intracellular enzyme abundances and bacterial growth: New evidences from the central carbon metabolism of Corynebacterium glutamicum.

PubMed

Noack, Stephan; Voges, Raphael; Gätgens, Jochem; Wiechert, Wolfgang

2017-09-20

Corynebacterium glutamicum serves as important production host for small molecular compounds that are derived from precursor molecules of the central carbon metabolism. It is therefore a well-studied model organism of industrial biotechnology. However, a deeper understanding of the regulatory principles underlying the synthesis of central metabolic enzymes under different environmental conditions as well as its impact on cell growth is still missing. We studied enzyme abundances in C. glutamicum in response to growth on: (i) one limiting carbon source by sampling chemostat and fed-batch cultivations and (ii) changing carbon sources provided in excess by sampling batch cultivations. The targeted quantification of 20 central metabolic enzymes by isotope dilution mass spectrometry revealed that cells maintain stable enzyme concentrations when grown on d-glucose as single carbon and energy source and, most importantly, independent of its availability. By contrast, switching from d-glucose to d-fructose, d-mannose, d-arabitol, acetate, l-lactate or l-glutamate results in highly specific enzyme regulation patterns that can partly be explained by the activity of known transcriptional regulators. Based on these experimental results we propose a simple framework for modeling cell population growth as a nested function of nutrient supply and intracellular enzyme abundances. In summary, our study extends the basis for the formulation of predictive mechanistic models of bacterial growth, applicable in industrial bioprocess development. Copyright © 2017 Elsevier B.V. All rights reserved.

Nitric oxide mediates antimicrobial peptide gene expression by activating eicosanoid signaling

PubMed Central

Sadekuzzaman, Md.

2018-01-01

Nitric oxide (NO) mediates both cellular and humoral immune responses in insects. Its mediation of cellular immune responses uses eicosanoids as a downstream signal. However, the cross-talk with two immune mediators was not known in humoral immune responses. This study focuses on cross-talk between two immune mediators in inducing gene expression of anti-microbial peptides (AMPs) of a lepidopteran insect, Spodoptera exigua. Up-regulation of eight AMPs was observed in S. exigua against bacterial challenge. However, the AMP induction was suppressed by injection of an NO synthase inhibitor, L-NAME, while little expressional change was observed on injecting its enantiomer, D-NAME. The functional association between NO biosynthesis and AMP gene expression was further supported by RNA interference (RNAi) against NO synthase (SeNOS), which suppressed AMP gene expression under the immune challenge. The AMP induction was also mimicked by NO alone because injecting an NO analog, SNAP, without bacterial challenge significantly induced the AMP gene expression. Interestingly, an eicosanoid biosynthesis inhibitor, dexamethasone (DEX), suppressed the NO induction of AMP expression. The inhibitory activity of DEX was reversed by the addition of arachidonic acid, a precursor of eicosanoid biosynthesis. AMP expression of S. exigua was also controlled by the Toll/IMD signal pathway. The RNAi of Toll receptors or Relish suppressed AMP gene expression by suppressing NO levels and subsequently reducing PLA2 enzyme activity. These results suggest that eicosanoids are a downstream signal of NO mediation of AMP expression against bacterial challenge. PMID:29466449

Influence of adhesion to activated carbon particles on the viability of waterborne pathogenic bacteria under flow.

PubMed

van der Mei, Henny C; Atema-Smit, Jelly; Jager, Debbie; Langworthy, Don E; Collias, Dimitris I; Mitchell, Michael D; Busscher, Henk J

2008-07-01

In rural areas around the world, people often rely on water filtration plants using activated carbon particles for safe water supply. Depending on the carbon surface, adhering microorganisms die or grow to form a biofilm. Assays to assess the efficacy of activated carbons in bacterial removal do not allow direct observation of bacterial adhesion and the determination of viability. Here we propose to use a parallel plate flow chamber with carbon particles attached to the bottom plate to study bacterial adhesion to individual carbon particles and determine the viability of adhering bacteria. Observation and enumeration is done after live/dead staining in a confocal laser scanning microscope. Escherichiae coli adhered in higher numbers than Raoultella terrigena, except to a coconut-based carbon, which showed low bacterial adhesion compared to other wood-based carbon types. After adhesion, 83-96% of the bacteria adhering to an acidic carbon were dead, while on a basic carbon 54-56% were dead. A positively charged, basic carbon yielded 76-78% bacteria dead, while on a negatively charged coconut-based carbon only 32-37% were killed upon adhesion. The possibility to determine both adhesion as well as the viability of adhering bacteria upon adhesion to carbon particles is most relevant, because if bacteria adhere but remain viable, this still puts the water treatment system at risk, as live bacteria can grow and form a biofilm that can then be shedded to cause contamination. (c) 2008 Wiley Periodicals, Inc.

Promotion of water-mediated carbon removal by nanostructured barium oxide/nickel interfaces in solid oxide fuel cells.

PubMed

Yang, Lei; Choi, YongMan; Qin, Wentao; Chen, Haiyan; Blinn, Kevin; Liu, Mingfei; Liu, Ping; Bai, Jianming; Tyson, Trevor A; Liu, Meilin

2011-06-21

The existing Ni-yttria-stabilized zirconia anodes in solid oxide fuel cells (SOFCs) perform poorly in carbon-containing fuels because of coking and deactivation at desired operating temperatures. Here we report a new anode with nanostructured barium oxide/nickel (BaO/Ni) interfaces for low-cost SOFCs, demonstrating high power density and stability in C(3)H(8), CO and gasified carbon fuels at 750°C. Synchrotron-based X-ray analyses and microscopy reveal that nanosized BaO islands grow on the Ni surface, creating numerous nanostructured BaO/Ni interfaces that readily adsorb water and facilitate water-mediated carbon removal reactions. Density functional theory calculations predict that the dissociated OH from H(2)O on BaO reacts with C on Ni near the BaO/Ni interface to produce CO and H species, which are then electrochemically oxidized at the triple-phase boundaries of the anode. This anode offers potential for ushering in a new generation of SOFCs for efficient, low-emission conversion of readily available fuels to electricity.

Promotion of water-mediated carbon removal by nanostructured barium oxide/nickel interfaces in solid oxide fuel cells

PubMed Central

Yang, Lei; Choi, YongMan; Qin, Wentao; Chen, Haiyan; Blinn, Kevin; Liu, Mingfei; Liu, Ping; Bai, Jianming; Tyson, Trevor A.; Liu, Meilin

2011-01-01

The existing Ni-yttria-stabilized zirconia anodes in solid oxide fuel cells (SOFCs) perform poorly in carbon-containing fuels because of coking and deactivation at desired operating temperatures. Here we report a new anode with nanostructured barium oxide/nickel (BaO/Ni) interfaces for low-cost SOFCs, demonstrating high power density and stability in C3H8, CO and gasified carbon fuels at 750°C. Synchrotron-based X-ray analyses and microscopy reveal that nanosized BaO islands grow on the Ni surface, creating numerous nanostructured BaO/Ni interfaces that readily adsorb water and facilitate water-mediated carbon removal reactions. Density functional theory calculations predict that the dissociated OH from H2O on BaO reacts with C on Ni near the BaO/Ni interface to produce CO and H species, which are then electrochemically oxidized at the triple-phase boundaries of the anode. This anode offers potential for ushering in a new generation of SOFCs for efficient, low-emission conversion of readily available fuels to electricity. PMID:21694705

Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin

PubMed Central

Byres, Emma; Paton, Adrienne W.; Paton, James C.; Löfling, Jonas C.; Smith, David F.; Wilce, Matthew C.J.; Talbot, Ursula M.; Chong, Damien C.; Yu, Hai; Huang, Shengshu; Chen, Xi; Varki, Nissi M.; Varki, Ajit; Rossjohn, Jamie; Beddoe, Travis

2009-01-01

AB5 toxins comprise an A subunit that corrupts essential eukaryotic cell functions, and pentameric B subunits that direct target cell uptake after binding surface glycans. Subtilase cytotoxin (SubAB) is an AB5 toxin secreted by Shiga toxigenic Escherichia coli (STEC)1, which causes serious gastrointestinal disease in humans2. SubAB causes haemolytic uraemic syndrome-like pathology in mice3 via SubA-mediated cleavage of BiP/GRP78, an essential endoplasmic reticulum chaperone4. Here we show that SubB has a strong preference for glycans terminating in the sialic acid N-glycolylneuraminic acid (Neu5Gc), a monosaccharide not synthesised in humans. Structures of SubB-Neu5Gc complexes revealed the basis for this specificity, and mutagenesis of key SubB residues abrogated in vitro glycan recognition, cell binding and cytotoxicity. SubAB specificity for Neu5Gc was confirmed using mouse tissues with a human-like deficiency of Neu5Gc and human cell lines fed with Neu5Gc. Despite human lack of Neu5Gc biosynthesis, assimilation of dietary Neu5Gc creates high-affinity receptors on human gut epithelia and kidney vasculature. This, together with the human lack of Neu5Gc-containing body fluid competitors, confers susceptibility to the gastrointestinal and systemic toxicities of SubAB. Ironically, foods rich in Neu5Gc are the most common source of STEC contamination. Thus a bacterial toxin’s receptor is generated by metabolic incorporation of an exogenous factor derived from food. PMID:18971931

Dissecting Bacterial Cell Wall Entry and Signaling in Eukaryotic Cells: an Actin-Dependent Pathway Parallels Platelet-Activating Factor Receptor-Mediated Endocytosis.

PubMed

Loh, Lip Nam; Gao, Geli; Tuomanen, Elaine I

2017-01-03

The Gram-positive bacterial cell wall (CW) peptidoglycan-teichoic acid complex is released into the host environment during bacterial metabolism or death. It is a highly inflammatory Toll-like receptor 2 (TLR2) ligand, and previous in vivo studies have demonstrated its ability to recapitulate pathological features of pneumonia and meningitis. We report that an actin-dependent pathway is involved in the internalization of the CW by epithelial and endothelial cells, in addition to the previously described platelet-activating factor receptor (PAFr)-dependent uptake pathway. Unlike the PAFr-dependent pathway, which is mediated by clathrin and dynamin and does not lead to signaling, the alternative pathway is sensitive to 5-(N-ethyl-N-isopropyl) amiloride (EIPA) and engenders Rac1, Cdc42, and phosphatidylinositol 3-kinase (PI3K) signaling. Upon internalization by this macropinocytosis-like pathway, CW is trafficked to lysosomes. Intracellular CW trafficking is more complex than previously recognized and suggests multiple points of interaction with and without innate immune signaling. Streptococcus pneumoniae is a major human pathogen infecting the respiratory tract and brain. It is an established model organism for understanding how infection injures the host. During infection or bacterial growth, bacteria shed their cell wall (CW) into the host environment and trigger inflammation. A previous study has shown that CW enters and crosses cell barriers by interacting with a receptor on the surfaces of host cells, termed platelet-activating factor receptor (PAFr). In the present study, by using cells that are depleted of PAFr, we identified a second pathway with features of macropinocytosis, which is a receptor-independent fluid uptake mechanism by cells. Each pathway contributes approximately the same amount of cell wall trafficking, but the PAFr pathway is silent, while the new pathway appears to contribute to the host inflammatory response to CW insult. Copyright © 2017

Rapid and efficient introduction of a foreign gene into bacterial artificial chromosome-cloned varicella vaccine by Tn7-mediated site-specific transposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somboonthum, Pranee; Koshizuka, Tetsuo; Okamoto, Shigefumi

2010-06-20

Using a rapid and reliable system based on Tn7-mediated site-specific transposition, we have successfully constructed a recombinant Oka varicella vaccine (vOka) expressing the mumps virus (MuV) fusion protein (F). The backbone of the vector was our previously reported vOka-BAC (bacterial artificial chromosome) genome. We inserted the transposon Tn7 attachment sequence, LacZ{alpha}-mini-attTn7, into the region between ORF12 and ORF13 to generate a vOka-BAC-Tn genome. The MuV-F expressing cassette was transposed into the vOka-BAC genome at the mini-attTn7 transposition site. MuV-F protein was expressed in recombinant virus, rvOka-F infected cells. In addition, the MuV-F protein was cleaved in the rvOka-F infected cellsmore » as in MuV-infected cells. The growth of rvOka-F was similar to that of the original recombinant vOka without the F gene. Thus, we show that Tn7-mediated transposition is an efficient method for introducing a foreign gene expression cassette into the vOka-BAC genome as a live virus vector.« less

On morphology of methane-derived authigenic carbonates

NASA Astrophysics Data System (ADS)

Logvina, E.; Matveeva, T.

2009-04-01

Studies of methane-derived carbonates revealed a great variety their morphological types. Although the processes of these carbonates formation is not clearly understood, it has been suggested that in general bacterially mediated processes of hydrocarbon oxidation, coupled with sulphate reduction, produce unusually high levels of alkalinity and dissolved inorganic carbon in the pore fluids that is partitioned between the precipitating carbonate and CO2 rich plumes which emanate into the water column (Aharon, 1994). These carbonates consist by three main CaCO3 polymorphs - calcite, aragonite and dolomite. Carbonates with different petrography cemented from these polymorphs can be classified according to their specific locality mode of formation and biogenic or non-biogenic origin (Greinert et al., 2002). There are classifications for the authigenic carbonates which are based on petrography, morphology, or based on age and origin. In this work we will consider the petrographical and morphological differences of authigenic carbonates. The large structures vary from 10 to 200 m size, named as chemoherm carbonates. Usually they cemented by pure aragonite with minor Mg-calcite admixture. These chemoherms rise up to 50 m above the seafloor. The structures are irregular in shape and have numerous pores and open pathways resulting from plumbing system of fluid expulsion. This type of authigenic carbonates was observed in the NE Black Sea (Michaelis et al., 2002), at the Hydrate Ridge area (Greinert et al., 2001), at Aleutian accretionary margin (Greinert et al., 2002). Diagenetic carbonates - carbonate cemented sediments both growing at the seafloor or within the sediment framework and showing a large variety of shapes (chimneys, crusts, concretions est.), with grey to dark-grey color. Petrographically the carbonate cement represents by Mg-calcite, protodolomite and dolomite. The diagenetic carbonates occur widely in the fluid venting areas. In particular, diagenetic

Effects of assimilable organic carbon and free chlorine on bacterial growth in drinking water.

PubMed

Liu, Xiaolu; Wang, Jingqi; Liu, Tingting; Kong, Weiwen; He, Xiaoqing; Jin, Yi; Zhang, Bolin

2015-01-01

Assimilable organic carbon (AOC) is one of the most important factors affecting the re-growth of microorganisms in drinking water. High AOC concentrations result in biological instability, but disinfection kills microbes to ensure the safety of drinking water. Free chlorine is an important oxidizing agent used during the disinfection process. Therefore, we explored the combined effects of AOC and free chlorine on bacterial growth in drinking water using flow cytometry (FCM). The initial AOC concentration was 168 μg.L(-1) in all water samples. Without free chlorine, the concentrations of intact bacteria increased but the level of AOC decreased. The addition of sodium hypochlorite caused an increase and fluctuation in AOC due to the oxidation of organic carbon. The concentrations of intact bacteria decreased from 1.1 × 10(5) cells.mL(-1) to 2.6 × 10(4) cells.mL(-1) at an initial free chlorine dose of 0.6 mg.L(-1) to 4.8 × 10(4) cells.mL(-1) at an initial free chlorine dose of 0.3 mg.L(-1) due to free chlorine originating from sodium hypochlorite. Additionally, free chlorine might be more obviously affected AOC concentrations than microbial growth did. These results suggested that AOC and free chlorine might have combined effects on microbial growth. In this study, our results showed concentrations determined by FCM were higher than those by HPC, which indicated that some E. coli detected by FCM might not be detected using HPC in drinking water. The level of free chlorine might restrain the consumption of AOC by inhibiting the growth of E. coli; on the other hand, chlorination might increase the level of AOC, thereby increase the potential for microbial growth in the drinking water network.

Effects of Assimilable Organic Carbon and Free Chlorine on Bacterial Growth in Drinking Water

PubMed Central

Liu, Tingting; Kong, Weiwen; He, Xiaoqing; Jin, Yi; Zhang, Bolin

2015-01-01

Assimilable organic carbon (AOC) is one of the most important factors affecting the re-growth of microorganisms in drinking water. High AOC concentrations result in biological instability, but disinfection kills microbes to ensure the safety of drinking water. Free chlorine is an important oxidizing agent used during the disinfection process. Therefore, we explored the combined effects of AOC and free chlorine on bacterial growth in drinking water using flow cytometry (FCM). The initial AOC concentration was 168 μg.L-1 in all water samples. Without free chlorine, the concentrations of intact bacteria increased but the level of AOC decreased. The addition of sodium hypochlorite caused an increase and fluctuation in AOC due to the oxidation of organic carbon. The concentrations of intact bacteria decreased from 1.1×105 cells.mL-1 to 2.6×104 cells.mL-1 at an initial free chlorine dose of 0.6 mg.L-1 to 4.8×104 cells.mL-1 at an initial free chlorine dose of 0.3 mg.L-1 due to free chlorine originating from sodium hypochlorite. Additionally, free chlorine might be more obviously affected AOC concentrations than microbial growth did. These results suggested that AOC and free chlorine might have combined effects on microbial growth. In this study, our results showed concentrations determined by FCM were higher than those by HPC, which indicated that some E. coli detected by FCM might not be detected using HPC in drinking water. The level of free chlorine might restrain the consumption of AOC by inhibiting the growth of E. coli; on the other hand, chlorination might increase the level of AOC, thereby increase the potential for microbial growth in the drinking water network. PMID:26034988

Synthesis of oxazolidine-2,4-diones by a tandem phosphorus-mediated carboxylative condensation-cyclization reaction using atmospheric carbon dioxide.

PubMed

Zhang, Wen-Zhen; Xia, Tian; Yang, Xu-Tong; Lu, Xiao-Bing

2015-04-11

The oxazolidine-2,4-dione motif is found frequently in biologically important compounds. A tandem phosphorus-mediated carboxylative condensation of primary amines and α-ketoesters/base-catalyzed cyclization reaction have been developed. These processes provide a novel and convenient access to various oxazolidine-2,4-diones in a one-pot fashion using atmospheric carbon dioxide and readily available substrates under very mild and transition-metal-free conditions.

Bacterial methane oxidation in sea-floor gas hydrate: Significance to life in extreme environments

NASA Astrophysics Data System (ADS)

Sassen, Roger; MacDonald, Ian R.; Guinasso, Norman L., Jr.; Joye, Samantha; Requejo, Adolfo G.; Sweet, Stephen T.; Alcalá-Herrera, Javier; Defreitas, Debra A.; Schink, David R.

1998-09-01

Samples of thermogenic hydrocarbon gases, from vents and gas hydrate mounds within a sea-floor chemosynthetic community on the Gulf of Mexico continental slope at about 540 m depth, were collected by research submersible. Our study area is characterized by low water temperature (mean =7 °C), high pressure (about 5400 kPa), and abundant structure II gas hydrate. Bacterial oxidation of hydrate-bound methane (CH4) is indicated by three isotopic properties of gas hydrate samples. Relative to the vent gas from which the gas hydrate formed, (1) methane-bound methane is enriched in 13C by as much as 3.8‰ PDB (Peedee belemnite), (2) hydrate-bound methane is enriched in deuterium (D) by as much as 37‰ SMOW (standard mean ocean water), and (3) hydrate-bound carbon dioxide (CO2) is depleted in 13C by as much as 22.4‰ PDB. Hydrate-associated authigenic carbonate rock is also depleted in 13C. Bacterial oxidation of methane is a driving force in chemosynthetic communities, and in the concomitant precipitation of authigenic carbonate rock that modifies sea-floor geology. Bacterial oxidation of hydrate-bound methane expands the potential boundaries of life in extreme environments.

Nanobiocomposite platform based on polyaniline-iron oxide-carbon nanotubes for bacterial detection.

PubMed

Singh, Renu; Verma, Rachna; Sumana, G; Srivastava, Avanish Kumar; Sood, Seema; Gupta, Rajinder K; Malhotra, B D

2012-08-01

The nanocomposite based on polyaniline (PANI)-iron oxide nanoparticles (nFe(3)O(4)) and multi walled carbon-nanotubes (CNT) has been fabricated onto indium tin oxide (ITO) coated glass plate via facile electrochemical synthesis of polyaniline in presence of nFe(3)O(4) (~20 nm) and CNT (20-80 nm in diameter). The results of transmission electron microscopic studies show evidence of coating of PANI and nFe(3)O(4) onto the CNT. The PANI-nFe(3)O(4)-CNT/ITO nanoelectrode has been characterized by Fourier transform infrared spectroscopy, X-ray diffraction and scanning electron microscopy studies. The biotinylated nucleic acid probe sequence consisting of 20 bases has been immobilized onto PANI-nFe(3)O(4)-CNT/ITO nanoelectrode using biotin-avidin coupling. It is shown that the PANI-nFe(3)O(4)-CNT platform based biosensor can be used to specifically detect bacteria (N. gonorrhoeae) at minute concentration as low as (1×10(-19) M) indicating high sensitivity within 45 s of hybridization time at 298 K by differential pulse voltammetry using methylene blue as electroactive indicator. This bacterial sensor has also been tested with 4 positive and 4 negative PCR amplicons of gonorrhoea affected patient samples. The results of these studies have implications towards the fabrication of a handheld device for Neisseria gonorrhoeae detection that may perhaps result in a decrease in the human immunodeficiency virus infections. Copyright © 2012 Elsevier B.V. All rights reserved.

Tobramycin mediated silver nanospheres/graphene oxide composite for synergistic therapy of bacterial infection.

PubMed

Ullah, Sadeeq; Ahmad, Aftab; Subhan, Fazli; Jan, Aminullah; Raza, Muslim; Khan, Arif Ullah; Rahman, Aziz-Ur; Khan, Usman Ali; Tariq, Muhammad; Yuan, Qipeng

2018-06-01

Graphene-based materials have attracted a significant attention in constructing hybrid systems for drug delivery with enhanced antimicrobial activities. In our work, we demonstrated the formation of silver nanoparticles (AgNPs) on graphene oxide (GO) using tobramycin (TOB), an aminoglycoside antibiotic, as reducing and decorating agent. The TOB decorated GO AgNPs (TOB-GO-Ag) composite was used as an antibacterial agent against multi-drug resistant Gram-negative E-coli (BL21 DE3). The reversal of surface potential from -30 mV (GO) to +20 mV confirms the successful reduction of GO by TOB. Atomic force microscopy (AFM) and high-resolution transmission electron microscopic (HRTEM) analyses confirmed the formation of uniformly distributed AgNPs on the reduced GO with an approximate particle size of 5 nm. The as-synthesized nanocomposite displayed significant antibacterial activity as compared to pure AgNPs and TOB. The positively charged TOB-GO-Ag interacts with the negatively charged E. coli membrane and inhibit bacterial growth by the antibacterial actions of the released silver, GO and tobramycin from the TOB-GO-Ag composite. The significant loss of bacterial membrane potential from -52 ± 2 mV (control) to -2 ± 1 mV (treated) indicates a severe cell wall damage caused by TOB-GO-Ag composite. Furthermore, fluorescence study also demonstrated a severe membrane disruption in bacterial cells treated with TOB-GO-Ag composite as compared to pure AgNPs and GO. In conclusion, the development of such hybrid systems would help in enhancing the efficacy of available drugs and eradicating the emerging bacterial resistance. Copyright © 2018 Elsevier B.V. All rights reserved.

Biofilm-mediated Antibiotic-resistant Oral Bacterial Infections: Mechanism and Combat Strategies.

PubMed

Kanwar, Indulata; Sah, Abhishek K; Suresh, Preeti K

2017-01-01

Oral diseases like dental caries and periodontal disease are directly associated with the capability of bacteria to form biofilm. Periodontal diseases have been associated to anaerobic Gram-negative bacteria forming a subgingival plaque (Porphyromonas gingivalis, Actinobacillus, Prevotella and Fusobacterium). Biofilm is a complex bacterial community that is highly resistant to antibiotics and human immunity. Biofilm communities are the causative agents of biological developments such as dental caries, periodontitis, peri-implantitis and causing periodontal tissue breakdown. The review recapitulates the latest advancements in treatment of clinical biofilm infections and scientific investigations, while these novel anti-biofilm strategies are still in nascent phases of development, efforts dedicated to these technologies could ultimately lead to anti-biofilm therapies that are superior to the current antibiotic treatment. This paper provides a review of the literature focusing on the studies on biofilm in the oral cavity, formation of dental plaque biofilm, drug resistance of bacterial biofilm and the antibiofilm approaches as biofilm preventive agents in dentistry, and their mechanism of biofilm inhibition. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Actin-mediated bacterial propulsion: comet profile, velocity pulsations.

PubMed

Benza, V G

2008-05-23

The propulsion of bacteria under the action of an actin gel network is examined in terms of gel concentration dynamics. The model includes the elasticity of the network, the gel-bacterium interaction, the bulk and interface polymerization. A formula for the cruise velocity is obtained where the contributions to bacterial motility arising from elasticity and polymerization are made explicit. Higher velocities correspond to lower concentration peaks and longer tails, in agreement with experimental results. The condition for the onset of motion is explicitly given. The behavior of the system is explored by varying the growth rates and the gel elasticity. At steady state two regimes are found, respectively, of constant and pulsating velocity; in the latter case, the velocity undergoes sudden accelerations and subsequent recoveries. The transition to the pulsating regime is obtained by increasing the elastic response of the gel.

Jellyfish modulate bacterial dynamic and community structure.

PubMed

Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

2012-01-01

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in

Single-cell measurement of archaeal and bacterial carbon assimilation in dark Pacific Ocean waters

NASA Astrophysics Data System (ADS)

Dekas, A. E.; Mayali, X.; Parada, A. E.; Fuhrman, J. A.; Weber, P. K.; Pett-Ridge, J.

2016-02-01

Microbial activity in the dark ocean plays a critical role in nutrient and elemental cycling. Here, we investigated the activity of archaea and bacteria on the single-cell level during dark incubations of Pacific Ocean water, and specifically their capacity for chemoautotrophy. Samples were collected 19 km off the coast of Los Angeles, at a depth of 150 m, and off the coast of San Francisco, at the surface. Incubations were amended with isotopically-labeled organic or inorganic carbon (13C-bicarbonate, 15N-amino acids or dual-labeled 13C-15N-amino acids), and uptake was detected using nanoscale secondary ion mass spectrometry (NanoSIMS). We analyzed 4,968 individual cells using an automated NanoSIMS analysis with particle-recognition software. After 7 days, 95% and 89% of cells (deep and shallow, respectively) demonstrated anabolic activity, i.e., incorporation of at least one isotopically-labeled substrate. Chemoautotrophy was detected at both sites, with 36% and 9% of cells (deep and shallow, respectively) assimilating 13C-bicarbonate in the dark. Fluorescence in situ hybridization coupled to NanoSIMS analysis was performed to link 16S rRNA phylogeny to patterns of C-assimilation. Thaumarchaea were found to dominate chemoautotrophy at both sites, with 13C-bicarbonate assimilation in nearly all cells hybridized with the Cren537 probe, but none hybridized with a general bacterial probe (Eub338). Conversely, widespread assimilation of both 15N and 13C from 15N-13C-amino acids was observed in the bacterial assemblage, but not in the Thaumarchaea. Interestingly, Thaumarchaeal cells were enriched in 15N after incubation with 15N-13C-amino acids, but not 13C, suggesting selective N assimilation from amino acids or substrate recycling. Together, our results demonstrate the value of single-cell measurements in characterizing patterns of C metabolism in mixed microbial community, and underscore the importance of Thaumarchaea in marine chemoautotrophy.

Carbonate precipitation under bulk acidic conditions as a potential biosignature for searching life on Mars

NASA Astrophysics Data System (ADS)

Fernández-Remolar, David C.; Preston, Louisa J.; Sánchez-Román, Mónica; Izawa, Matthew R. M.; Huang, L.; Southam, Gordon; Banerjee, Neil R.; Osinski, Gordon R.; Flemming, Roberta; Gómez-Ortíz, David; Prieto Ballesteros, Olga; Rodríguez, Nuria; Amils, Ricardo; Darby Dyar, M.

2012-10-01

Recent observations of carbonate minerals in ancient Martian rocks have been interpreted as evidence for the former presence of circumneutral solutions optimal for carbonate precipitation. Sampling from surface and subsurface regions of the low-pH system of Río Tinto has shown, unexpectedly, that carbonates can form under diverse macroscopic physicochemical conditions ranging from very low to neutral pH (1.5-7.0). A multi-technique approach demonstrates that carbonate minerals are closely associated with microbial activity. Carbonates occur in the form of micron-size carbonate precipitates under bacterial biofilms, mineralization of subsurface colonies, and possible biogenic microstructures including globules, platelets and dumbbell morphologies. We propose that carbonate precipitation in the low-pH environment of Río Tinto is a process enabled by microbially-mediated neutralization driven by the reduction of ferric iron coupled to the oxidation of biomolecules in microbially-maintained circumneutral oases, where the local pH (at the scale of cells or cell colonies) can be much different than in the macroscopic environment. Acidic conditions were likely predominant in vast regions of Mars over the last four billion years of planetary evolution. Ancient Martian microbial life inhabiting low-pH environments could have precipitated carbonates similar to those observed at Río Tinto. Preservation of carbonates at Río Tinto over geologically significant timescales suggests that similarly-formed carbonate minerals could also be preserved on Mars. Such carbonates could soon be observed by the Mars Science Laboratory, and by future missions to the red planet.

An active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community.

PubMed

Eronen-Rasimus, Eeva; Luhtanen, Anne-Mari; Rintala, Janne-Markus; Delille, Bruno; Dieckmann, Gerhard; Karkman, Antti; Tison, Jean-Louis

2017-10-01

Antarctic sea-ice bacterial community composition and dynamics in various developmental stages were investigated during the austral winter in 2013. Thick snow cover likely insulated the ice, leading to high (<4 μg l -1 ) chlorophyll-a (chl-a) concentrations and consequent bacterial production. Typical sea-ice bacterial genera, for example, Octadecabacter, Polaribacter and Glaciecola, often abundant in spring and summer during the sea-ice algal bloom, predominated in the communities. The variability in bacterial community composition in the different ice types was mainly explained by the chl-a concentrations, suggesting that as in spring and summer sea ice, the sea-ice bacteria and algae may also be coupled during the Antarctic winter. Coupling between the bacterial community and sea-ice algae was further supported by significant correlations between bacterial abundance and production with chl-a. In addition, sulphate-reducing bacteria (for example, Desulforhopalus) together with odour of H 2 S were observed in thick, apparently anoxic ice, suggesting that the development of the anaerobic bacterial community may occur in sea ice under suitable conditions. In all, the results show that bacterial community in Antarctic sea ice can stay active throughout the winter period and thus possible future warming of sea ice and consequent increase in bacterial production may lead to changes in bacteria-mediated processes in the Antarctic sea-ice zone.

Relationships between soil organic matter, nutrients, bacterial community structure, and the performance of microbial fuel cells.

PubMed

Dunaj, Sara J; Vallino, Joseph J; Hines, Mark E; Gay, Marcus; Kobyljanec, Christine; Rooney-Varga, Juliette N

2012-02-07

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful renewable resource: soil organic carbon. We analyzed bacterial community structure, MFC performance, and soil characteristics in different microhabitats within MFCs constructed from agricultural or forest soils in order to determine how soil type and bacterial dynamics influence MFC performance. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs. Bacterial community profile data indicate that the bacterial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These results suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic bacterial communities, while the quality of available organic matter may have played a significant role in supporting high performing bacterial communities.

Effect of disinfectant residual on the interaction between bacterial growth and assimilable organic carbon in a drinking water distribution system.

PubMed

Li, Weiying; Zhang, Junpeng; Wang, Feng; Qian, Lin; Zhou, Yanyan; Qi, Wanqi; Chen, Jiping

2018-07-01

Public health is threatened by deteriorated water quality due to bacterial regrowth and uncontrolled growth-related problems in drinking water distribution systems (DWDSs). To investigate the scope of this problem, a two-year field study was conducted in south China. The amount of assimilable organic carbon (AOC), total cell concentrations (TCC), and intact cell concentrations (ICC) of water samples were determined by flow cytometry. The results indicated that ICC was significantly correlated to AOC concentration when the chlorine concentration was less than 0.15 mg/L, and ICC was lower at chlorine concentrations greater than 0.15 mg/L, suggesting that free chlorine level had effect on AOC and ICC. To further analyze the effect of disinfectant on AOC and bacterial growth, we designed an orthogonal experiment with different dosages of two commonly used disinfectants, chlorine and chloramine. The results demonstrated that high concentrations of free chlorine (＞0.15 mg/L) and chloramine (＞0.4 mg/L) were associated with relatively low proportions of intact cells and cultivable bacteria. Compared with chlorine, chloramine tended to cause lower AOC level and intact cells, likely because the chlorinated disinfection byproducts (DBPs) were more easily absorbed by bacteria than the chloraminated DBPs. Based on the statistical analysis of 240 water samples, ICC was limited when AOC concentration was less than 135 μg/L, while temperature and the number of small-size particles showed positive effects on ICC (P＜0.05). We conclude that the use of chloramine and controlling particle numbers should be suitable strategies to limit bacterial regrowth. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bacterial Adaptation to Antibiotics through Regulatory RNAs.

PubMed

Felden, Brice; Cattoir, Vincent

2018-05-01

The extensive use of antibiotics has resulted in a situation where multidrug-resistant pathogens have become a severe menace to human health worldwide. A deeper understanding of the principles used by pathogens to adapt to, respond to, and resist antibiotics would pave the road to the discovery of drugs with novel mechanisms. For bacteria, antibiotics represent clinically relevant stresses that induce protective responses. The recent implication of regulatory RNAs (small RNAs [sRNAs]) in antibiotic response and resistance in several bacterial pathogens suggests that they should be considered innovative drug targets. This minireview discusses sRNA-mediated mechanisms exploited by bacterial pathogens to fight against antibiotics. A critical discussion of the newest findings in the field is provided, with emphasis on the implication of sRNAs in major mechanisms leading to antibiotic resistance, including drug uptake, active drug efflux, drug target modifications, biofilms, cell walls, and lipopolysaccharide (LPS) biosynthesis. Of interest is the lack of knowledge about sRNAs implicated in Gram-positive compared to Gram-negative bacterial resistance. Copyright © 2018 American Society for Microbiology.

Probing Prokaryotic Social Behaviors with Bacterial “Lobster Traps”

PubMed Central

Connell, Jodi L.; Wessel, Aimee K.; Parsek, Matthew R.; Ellington, Andrew D.; Whiteley, Marvin; Shear, Jason B.

2010-01-01

Bacteria are social organisms that display distinct behaviors/phenotypes when present in groups. These behaviors include the abilities to construct antibiotic-resistant sessile biofilm communities and to communicate with small signaling molecules (quorum sensing [QS]). Our understanding of biofilms and QS arises primarily from in vitro studies of bacterial communities containing large numbers of cells, often greater than 108 bacteria; however, in nature, bacteria often reside in dense clusters (aggregates) consisting of significantly fewer cells. Indeed, bacterial clusters containing 101 to 105 cells are important for transmission of many bacterial pathogens. Here, we describe a versatile strategy for conducting mechanistic studies to interrogate the molecular processes controlling antibiotic resistance and QS-mediated virulence factor production in high-density bacterial clusters. This strategy involves enclosing a single bacterium within three-dimensional picoliter-scale microcavities (referred to as bacterial “lobster traps”) defined by walls that are permeable to nutrients, waste products, and other bioactive small molecules. Within these traps, bacteria divide normally into extremely dense (1012 cells/ml) clonal populations with final population sizes similar to that observed in naturally occurring bacterial clusters. Using these traps, we provide strong evidence that within low-cell-number/high-density bacterial clusters, QS is modulated not only by bacterial density but also by population size and flow rate of the surrounding medium. We also demonstrate that antibiotic resistance develops as cell density increases, with as few as ~150 confined bacteria exhibiting an antibiotic-resistant phenotype similar to biofilm bacteria. Together, these findings provide key insights into clinically relevant phenotypes in low-cell-number/high-density bacterial populations. PMID:21060734

Direct and mediated electrochemistry of peroxidase and its electrocatalysis on a variety of screen-printed carbon electrodes: amperometric hydrogen peroxide and phenols biosensor.

PubMed

Chekin, Fereshteh; Gorton, Lo; Tapsobea, Issa

2015-01-01

This study compares the behaviour of direct and mediated electrochemistry of horseradish peroxidase (HRP) immobilised on screen-printed carbon electrodes (SPCEs), screen-printed carbon electrodes modified with carboxyl-functionalised multi-wall carbon nanotubes (MWCNT-SPCEs) and screen-printed carbon electrodes modified with carboxyl-functionalised single-wall carbon nanotubes (SWCNT-SPCEs). The techniques of cyclic voltammetry and amperometry in the flow mode were used to characterise the properties of the HRP immobilised on screen-printed electrodes. From measurements of the mediated and mediatorless currents of hydrogen peroxide reduction at the HRP-modified electrodes, it was concluded that the fraction of enzyme molecules in direct electron transfer (DET) contact with the electrode varies substantially for the different electrodes. It was observed that the screen-printed carbon electrodes modified with carbon nanotubes (MWCNT-SPCEs and SWCNT-SPCEs) demonstrated a substantially higher percentage (≈100 %) of HRP molecules in DET contact than the screen-printed carbon electrodes (≈60 %). The HRP-modified electrodes were used for determination of hydrogen peroxide in mediatorless mode. The SWCNT-SPCE gave the lowest detection limit (0.40 ± 0.09 μM) followed by MWCNT-SPCE (0.48 ± 0.07 μM) and SPCE (0.98 ± 0.2 μM). These modified electrodes were additionally developed for amperometric determination of phenolic compounds. It was found that the SWCNT-SPCE gave a detection limit for catechol of 110.2 ± 3.6 nM, dopamine of 640.2 ± 9.2 nM, octopamine of 3341 ± 15 nM, pyrogallol of 50.10 ± 2.9 nM and 3,4-dihydroxy-L-phenylalanine of 980.7 ± 8.7 nM using 50 μM H2O2 in the flow carrier.

Bacterial Dispersal Promotes Biodegradation in Heterogeneous Systems Exposed to Osmotic Stress

PubMed Central

Worrich, Anja; König, Sara; Banitz, Thomas; Centler, Florian; Frank, Karin; Thullner, Martin; Harms, Hauke; Miltner, Anja; Wick, Lukas Y.; Kästner, Matthias

2016-01-01

Contaminant biodegradation in soils is hampered by the heterogeneous distribution of degrading communities colonizing isolated microenvironments as a result of the soil architecture. Over the last years, soil salinization was recognized as an additional problem especially in arid and semiarid ecosystems as it drastically reduces the activity and motility of bacteria. Here, we studied the importance of different spatial processes for benzoate biodegradation at an environmentally relevant range of osmotic potentials (ΔΨo) using model ecosystems exhibiting a heterogeneous distribution of the soil-borne bacterium Pseudomonas putida KT2440. Three systematically manipulated scenarios allowed us to cover the effects of (i) substrate diffusion, (ii) substrate diffusion and autonomous bacterial dispersal, and (iii) substrate diffusion and autonomous as well as mediated bacterial dispersal along glass fiber networks mimicking fungal hyphae. To quantify the relative importance of the different spatial processes, we compared these heterogeneous scenarios to a reference value obtained for each ΔΨo by means of a quasi-optimal scenario in which degraders were ab initio homogeneously distributed. Substrate diffusion as the sole spatial process was insufficient to counteract the disadvantage due to spatial degrader heterogeneity at ΔΨo ranging from 0 to −1 MPa. In this scenario, only 13.8−21.3% of the quasi-optimal biodegradation performance could be achieved. In the same range of ΔΨo values, substrate diffusion in combination with bacterial dispersal allowed between 68.6 and 36.2% of the performance showing a clear downwards trend with decreasing ΔΨo. At −1.5 MPa, however, this scenario performed worse than the diffusion scenario, possibly as a result of energetic disadvantages associated with flagellum synthesis and emerging requirements to exceed a critical population density to resist osmotic stress. Network-mediated bacterial dispersal kept biodegradation

Assessment of carbon nanotubes and silver nanoparticles loaded clays as adsorbents for removal of bacterial contaminants from water sources.

PubMed

Hassouna, M E M; ElBably, M A; Mohammed, Asmaa N; Nasser, M A G

2017-02-01

This work evaluated the antimicrobial efficacy of kaolin clay and its loaded forms with carbon nanotubes (CNTs) and silver nanoparticles (AgNPs) against bacterial isolates from different water supplies (tap, underground and surface water) in addition to wastewater. A total of 160 water samples were collected from different water sources in the investigated districts. Samples were cultured for isolation and serological identification of pathogenic bacteria. AgNPs were synthesized by a typical one-step synthesis protocol, where CNTs were carried out in a reactor employing the double bias-assisted hot filament chemical vapor deposition method. Both were characterized using transmission electron microscopy, infrared and X-ray fluorescence (XRF) spectroscopy. The antimicrobial efficacy of each of natural kaolin clay, AgNPs- and CNTs-loaded clays were evaluated by their application in four concentrations (0.01, 0.03, 0.05 and 0.1 ppm) at different contact times (5 min, 15 min, 30 min and 2 h). AgNPs-loaded clays at concentrations of 0.05 and 0.1 mg/l for 2 h contact time exhibited a higher bactericidal efficacy on Escherichia coli and Salmonella spp. (70, 70, 80 and 90%, respectively) compared to CNTs-loaded clay. Concluding, the application of AgNPs-loaded clay for removal of water bacterial contaminants at a concentration of 0.1 ppm for 2 h contact times resulted in highly effective removals.

Nano-twin Mediated Plasticity in Carbon-containing FeNiCoCrMn High Entropy Alloys

DOE PAGES

Wu, Zhenggang; Bei, Hongbin; Parish, Chad M

2015-06-14

Equiatomic FeNiCoCrMn alloy has been reported to exhibit promising strength and ductility at cryogenic temperature and deformation mediated by nano-twining appeared to be one of the main reasons. We use the FeNiCoCrMn alloy as a base alloy to seek further improvement of its mechanical properties by alloying additional elements, i.e., interstitial carbon. Moreover, the effects of carbon on microstructures, mechanical properties and twinning activities were investigated in two different temperatures (77 and 293 K). With addition of 0.5 at% C, the high entropy alloy still remains entirely single phase face-centered cubic (FCC) crystal structure. We found that these materials canmore » be cold rolled and recrystallized to produce a microstructure with equiaxed grains. Both strain hardening rate and strength are enhanced while high uniform elongations to fracture (~70% at 77 K and ~40% at 293 K) are still maintained. The increased strain hardening and strength could be caused by the promptness of deformation twinning in C-containing high entropy alloys.« less

Suppression of bacterial infection in rice by treatment with a sulfated peptide.

PubMed

Wei, Tong; Chern, Mawsheng; Liu, Furong; Ronald, Pamela C

2016-12-01

The rice XA21 receptor kinase confers robust resistance to bacterial blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo). A tyrosine-sulfated peptide from Xoo, called RaxX, triggers XA21-mediated immune responses, including the production of ethylene and reactive oxygen species and the induction of defence gene expression. It has not been tested previously whether these responses confer effective resistance to Xoo. Here, we describe a newly established post-inoculation treatment assay that facilitates investigations into the effect of the sulfated RaxX peptide in planta. In this assay, rice plants were inoculated with a virulent strain of Xoo and then treated with the RaxX peptide 2 days after inoculation. We found that post-inoculation treatment of XA21 plants with the sulfated RaxX peptide suppresses the development of Xoo infection in XA21 rice plants. The treated plants display restricted lesion development and reduced bacterial growth. Our findings demonstrate that exogenous application of sulfated RaxX activates XA21-mediated immunity in planta, and provides a potential strategy for the control of bacterial disease in the field. © 2016 BSPP and John Wiley & Sons Ltd.

Bacterial Mercury Methylation At The Sediment-Water Interface Of Mercury Contaminated Sediments

EPA Science Inventory

Bench scale experiments were conducted to improve our understanding of bacterial mediation of mercury transformation (methylation), specifically those factors which govern the production of methyl mercury (MeHg) at the sediment-water interface. The greatest cause for concern re...

Flexible and Freestanding Supercapacitor Electrodes Based on Nitrogen-Doped Carbon Networks/Graphene/Bacterial Cellulose with Ultrahigh Areal Capacitance.

PubMed

Ma, Lina; Liu, Rong; Niu, Haijun; Xing, Lixin; Liu, Li; Huang, Yudong

2016-12-14

Flexible energy-storage devices based on supercapacitors rely largely on the scrupulous design of flexible electrodes with both good electrochemical performance and high mechanical properties. Here, nitrogen-doped carbon nanofiber networks/reduced graphene oxide/bacterial cellulose (N-CNFs/RGO/BC) freestanding paper is first designed as a high-performance, mechanically tough, and bendable electrode for a supercapacitor. The BC is exploited as both a supporting substrate for a large mass loading of 8 mg cm -2 and a biomass precursor for N-CNFs by pyrolysis. The one-step carbonization treatment not only fabricates the nitrogen-doped three-dimensional (3D) nanostructured carbon composite materials but also forms the reduction of the GO sheets at the same time. The fabricated paper electrode exhibits an ultrahigh areal capacitance of 2106 mF cm -2 (263 F g -1 ) in a KOH electrolyte and 2544 mF cm -2 (318 F g -1 ) in a H 2 SO 4 electrolyte, exceptional cycling stability (∼100% retention after 20000 cycles), and excellent tensile strength (40.7 MPa). The symmetric supercapacitor shows a high areal capacitance (810 mF cm -2 in KOH and 920 mF cm -2 in H 2 SO 4 ) and thus delivers a high energy density (0.11 mWh cm -2 in KOH and 0.29 mWh cm -2 in H 2 SO 4 ) and a maximum power density (27 mW cm -2 in KOH and 37.5 mW cm -2 in H 2 SO 4 ). This work shows that the new procedure is a powerful and promising way to design flexible and freestanding supercapacitor electrodes.

The role of magnetic iron oxide nanoparticles in the bacterially induced calcium carbonate precipitation.

PubMed

Seifan, Mostafa; Ebrahiminezhad, Alireza; Ghasemi, Younes; Samani, Ali Khajeh; Berenjian, Aydin

2018-04-01

Recently, magnetic iron oxide nanoparticles (IONs) have been used to control and modify the characteristics of concrete and mortar. Concrete is one of the most used materials in the world; however, it is susceptible to cracking. Over recent years, a sustainable biotechnological approach has emerged as an alternative approach to conventional techniques to heal the concrete cracks by the incorporation of bacterial cells and nutrients into the concrete matrix. Once cracking occurs, CaCO 3 is induced and the crack is healed. Considering the positive effects of IONs on the concrete properties, the effect of these nanoparticles on bacterial growth and CaCO 3 biosynthesis needs to be evaluated for their possible application in bio self-healing concrete. In the present work, IONs were successfully synthesized and characterized using various techniques. The presence of IONs showed a significant effect on both bacterial growth and CaCO 3 precipitation. The highest bacterial growth was observed in the presence of 150 μg/mL IONs. The highest concentration of induced CaCO 3 (34.54 g/L) was achieved when the bacterial cells were immobilized with 300 μg/mL of IONs. This study provides new data and supports the possibility of using IONs as a new tool in designing the next generation of bio self-healing concrete.

Synergistic effects of UVR and simulated stratification on commensalistic algal-bacterial relationship in two optically contrasting oligotrophic Mediterranean lakes

NASA Astrophysics Data System (ADS)

Carrillo, P.; Medina-Sánchez, J. M.; Durán, C.; Herrera, G.; Villafañe, V. E.; Helbling, E. W.

2014-08-01

An indirect effect of global warming is the shallowing epilimnion, causing organisms to be exposed to higher levels of ultraviolet (UVR, 280-400 nm) and photosynthetically active radiation (PAR, 400-700 nm), which could affect primary and bacterial production as well as the commensalistic algal-bacterial relationship. The combined effects of UVR and reduction in the depth of the upper mixed layer (UML) were assessed on variables related to the metabolism of algae and bacteria, during in situ experiments performed with natural microplanktonic communities from two oligotrophic lakes with contrasting UVR-transparency (clear vs. opaque) of southern Spain. The negative UVR effects on epilimnetic primary production (PP) and on heterotrophic bacterial production (HBP), intensified by high mean irradiances, were higher in the UVR-opaque than in the UVR-clear lake, and stronger on the algae than on the heterotrophic bacterial communities. Under UVR and high mean irradiance, the algal-bacterial relationship was strengthened in the UVR-clear lake, where excreted organic carbon (EOC) rates exceeded the bacterial carbon demand (BCD). This did not occur in the UVR-opaque lake. The greater UVR damage to algae and bacteria and the weakening of their commensalistic interaction found in the UVR-opaque lake indicates that these ecosystems would be especially vulnerable to stressors related to global change. Thus, our findings may have important implications for the carbon cycle in oligotrophic lakes of the Mediterranean region.

Trends, application and future prospectives of microbial carbonic anhydrase mediated carbonation process for CCUS.

PubMed

Bhagat, C; Dudhagara, P; Tank, S

2018-02-01

Growing industrialization and the desire for a better economy in countries has accelerated the emission of greenhouse gases (GHGs), by more than the buffering capacity of the earth's atmosphere. Among the various GHGs, carbon dioxide occupies the first position in the anthroposphere and has detrimental effects on the ecosystem. For decarbonization, several non-biological methods of carbon capture, utilization and storage (CCUS) have been in use for the past few decades, but they are suffering from narrow applicability. Recently, CO 2 emission and its disposal related problems have encouraged the implementation of bioprocessing to achieve a zero waste economy for a sustainable environment. Microbial carbonic anhydrase (CA) catalyses reversible CO 2 hydration and forms metal carbonates that mimic the natural phenomenon of weathering/carbonation and is gaining merit for CCUS. Thus, the diversity and specificity of CAs from different micro-organisms could be explored for CCUS. In the literature, more than 50 different microbial CAs have been explored for mineral carbonation. Further, microbial CAs can be engineered for the mineral carbonation process to develop new technology. CA driven carbonation is encouraging due to its large storage capacity and favourable chemistry, allowing site-specific sequestration and reusable product formation for other industries. Moreover, carbonation based CCUS holds five-fold more sequestration capacity over the next 100 years. Thus, it is an eco-friendly, feasible, viable option and believed to be the impending technology for CCUS. Here, we attempt to examine the distribution of various types of microbial CAs with their potential applications and future direction for carbon capture. Although there are few key challenges in bio-based technology, they need to be addressed in order to commercialize the technology. © 2017 The Society for Applied Microbiology.

Load-dependent assembly of the bacterial flagellar motor.

PubMed

Tipping, Murray J; Delalez, Nicolas J; Lim, Ren; Berry, Richard M; Armitage, Judith P

2013-08-20

It is becoming clear that the bacterial flagellar motor output is important not only for bacterial locomotion but also for mediating the transition from liquid to surface living. The output of the flagellar motor changes with the mechanical load placed on it by the external environment: at a higher load, the motor runs more slowly and produces higher torque. Here we show that the number of torque-generating units bound to the flagellar motor also depends on the external mechanical load, with fewer stators at lower loads. Stalled motors contained at least as many stators as rotating motors at high load, indicating that rotation is unnecessary for stator binding. Mutant stators incapable of generating torque could not be detected around the motor. We speculate that a component of the bacterial flagellar motor senses external load and mediates the strength of stator binding to the rest of the motor. The transition between liquid living and surface living is important in the life cycles of many bacteria. In this paper, we describe how the flagellar motor, used by bacteria for locomotion through liquid media and across solid surfaces, is capable of adjusting the number of bound stator units to better suit the external load conditions. By stalling motors using external magnetic fields, we also show that rotation is not required for maintenance of stators around the motor; instead, torque production is the essential factor for motor stability. These new results, in addition to previous data, lead us to hypothesize that the motor stators function as mechanosensors as well as functioning as torque-generating units.

Biomimetic CO2 capture using a highly thermostable bacterial α-carbonic anhydrase immobilized on a polyurethane foam.

PubMed

Migliardini, Fortunato; De Luca, Viviana; Carginale, Vincenzo; Rossi, Mosè; Corbo, Pasquale; Supuran, Claudiu T; Capasso, Clemente

2014-02-01

The biomimetic approach represents an interesting strategy for carbon dioxide (CO2) capture, offering advantages over other methods, due to its specificity for CO2 and its eco-compatibility, as it allows concentration of CO2 from other gases, and its conversion to water soluble ions. This approach uses microorganisms capable of fixing CO2 through metabolic pathways or via the use of an enzyme, such as carbonic anhydrase (CA, EC 4.2.1.1). Recently, our group cloned and purified a novel bacterial α-CA, named SspCA, from the thermophilic bacteria, Sulfurihydrogenibium yellowstonense YO3AOP1 living in hot springs at temperatures of up to 110 °C. This enzyme showed an exceptional thermal stability, retaining its high catalytic activity for the CO2 hydration reaction even after being heated at 70 °C for several hours. In the present paper, the SspCA was immobilized within a polyurethane (PU) foam. The immobilized enzyme was found to be catalytically active and showed a long-term stability. A bioreactor containing the "PU-immobilized enzyme" (PU-SspCA) as shredded foam was used for experimental tests aimed to verify the CO2 capture capability in conditions close to those of a power plant application. In this bioreactor, a gas phase, containing CO2, was put into contact with a liquid phase under conditions, where CO2 contained in the gas phase was absorbed and efficiently converted into bicarbonate by the extremo-α-CA.

Comparative Genomic Analyses of the Bacterial Phosphotransferase System

PubMed Central

Barabote, Ravi D.; Saier, Milton H.

2005-01-01

We report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS). These included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. Homologues of PTS proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding PTS proteins has not occurred between the three domains of life. Of the 174 bacterial genomes (136 bacterial species) analyzed, 30 diverse species have no PTS homologues, and 29 species have cytoplasmic PTS phosphoryl transfer protein homologues but lack recognizable PTS permeases. These soluble homologues presumably function in regulation. The remaining 77 species possess all PTS proteins required for the transport and phosphorylation of at least one sugar via the PTS. Up to 3.2% of the genes in a bacterium encode PTS proteins. These homologues were analyzed for family association, range of protein types, domain organization, and organismal distribution. Different strains of a single bacterial species often possess strikingly different complements of PTS proteins. Types of PTS protein domain fusions were analyzed, showing that certain types of domain fusions are common, while others are rare or prohibited. Select PTS proteins were analyzed from different phylogenetic standpoints, showing that PTS protein phylogeny often differs from organismal phylogeny. The results document the frequent gain and loss of PTS protein-encoding genes and suggest that the lateral transfer of these genes within the bacterial domain has played an important role in bacterial evolution. Our studies provide insight into the development of complex multicomponent enzyme systems and lead to predictions regarding the types of protein-protein interactions that promote efficient PTS-mediated phosphoryl transfer. PMID:16339738

Control of bacterial adhesion and growth on honeycomb-like patterned surfaces.

PubMed

Yang, Meng; Ding, Yonghui; Ge, Xiang; Leng, Yang

2015-11-01

It is a great challenge to construct a persistent bacteria-resistant surface even though it has been demonstrated that several surface features might be used to control bacterial behavior, including surface topography. In this study, we develop micro-scale honeycomb-like patterns of different sizes (0.5-10 μm) as well as a flat area as the control on a single platform to evaluate the bacterial adhesion and growth. Bacteria strains, Escherichia coli and Staphylococcus aureus with two distinct shapes (rod and sphere) are cultured on the platforms, with the patterned surface-up and surface-down in the culture medium. The results demonstrate that the 1 μm patterns remarkably reduce bacterial adhesion and growth while suppressing bacterial colonization when compared to the flat surface. The selective adhesion of the bacterial cells on the patterns reveals that the bacterial adhesion is cooperatively mediated by maximizing the cell-substrate contact area and minimizing the cell deformation, from a thermodynamic point of view. Moreover, study of bacterial behaviors on the surface-up vs. surface-down samples shows that gravity does not apparently affect the spatial distribution of the adherent cells although it indeed facilitates bacterial adhesion. Furthermore, the experimental results suggest that two major factors, i.e. the availability of energetically favorable adhesion sites and the physical confinements, contribute to the anti-bacterial nature of the honeycomb-like patterns. Copyright © 2015 Elsevier B.V. All rights reserved.

Isolation and identification of efficient Egyptian malathion-degrading bacterial isolates.

PubMed

Hamouda, S A; Marzouk, M A; Abbassy, M A; Abd-El-Haleem, D A; Shamseldin, Abdelaal

2015-03-01

Bacterial isolates degrading malathion were isolated from the soil and agricultural waste water due to their ability to grow on minimal salt media amended with malathion as a sole carbon source. Efficiencies of native Egyptian bacterial malathion-degrading isolates were investigated and the study generated nine highly effective malathion-degrading bacterial strains among 40. Strains were identified by partial sequencing of 16S rDNA analysis. Comparative analysis of 16S rDNA sequences revealed that these bacteria are similar with the genus Acinetobacter and Bacillus spp. and RFLP based PCR of 16S rDNA gave four different RFLP patterns among strains with enzyme HinfI while with enzyme HaeI they gave two RFLP profiles. The degradation rate of malathion in liquid culture was estimated using gas chromatography. Bacterial strains could degrade more than 90% of the initial malathion concentration (1000 ppm) within 4 days. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Molecular Density of States in Bacterial Nanowires

PubMed Central

El-Naggar, Mohamed Y.; Gorby, Yuri A.; Xia, Wei; Nealson, Kenneth H.

2008-01-01

The recent discovery of electrically conductive bacterial appendages has significant physiological, ecological, and biotechnological implications, but the mechanism of electron transport in these nanostructures remains unclear. We here report quantitative measurements of transport across bacterial nanowires produced by the dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, whose electron transport system is being investigated for renewable energy recovery in microbial fuel cells and bioremediation of heavy metals and radionuclides. The Shewanella nanowires display a surprising nonlinear electrical transport behavior, where the voltage dependence of the conductance reveals peaks indicating discrete energy levels with higher electronic density of states. Our results indicate that the molecular constituents along the Shewanella nanowires possess an intricate electronic structure that plays a role in mediating transport. PMID:18441026

Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China.

PubMed

Xun, Weibing; Zhao, Jun; Xue, Chao; Zhang, Guishan; Ran, Wei; Wang, Boren; Shen, Qirong; Zhang, Ruifu

2016-06-01

Different fertilization managements of red soil, a kind of Ferralic Cambisol, strongly affected the soil properties and associated microbial communities. The association of the soil microbial community and functionality with long-term fertilization management in the unique low-productivity red soil ecosystem is important for both soil microbial ecology and agricultural production. Here, 454 pyrosequencing analysis of 16S recombinant ribonucleic acid genes and GeoChip4-NimbleGen-based functional gene analysis were used to study the soil bacterial community composition and functional genes involved in soil organic carbon degradation. Long-term nitrogen-containing chemical fertilization-induced soil acidification and fertility decline and significantly altered the soil bacterial community, whereas long-term organic fertilization and fallow management improved the soil quality and maintained the bacterial diversity. Short-term quicklime remediation of the acidified soils did not change the bacterial communities. Organic fertilization and fallow management supported eutrophic ecosystems, in which copiotrophic taxa increased in relative abundance and have a higher intensity of labile-C-degrading genes. However, long-term nitrogen-containing chemical fertilization treatments supported oligotrophic ecosystems, in which oligotrophic taxa increased in relative abundance and have a higher intensity of recalcitrant-C-degrading genes but a lower intensity of labile-C-degrading genes. Quicklime application increased the relative abundance of copiotrophic taxa and crop production, although these effects were utterly inadequate. This study provides insights into the interaction of soil bacterial communities, soil functionality and long-term fertilization management in the red soil ecosystem; these insights are important for improving the fertility of unique low-productivity red soil. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Thin Layer Drying Model of Bacterial Cellulose Film

NASA Astrophysics Data System (ADS)

Hadi Jatmiko, Tri; Taufika Rosyida, Vita; Wheni Indrianingsih, Anastasia; Apriyana, Wuri

2017-12-01

The bacterial cellulose film produced by Acetobacter xylinum using coconut water as a carbon source was dried at a temperature of 60 to 100 C. The drying process of bacterial cellulose film occur at falling rate drying period. Increasing drying temperature will shorten the drying time. The drying data fitted with thin layer drying models that widely used, Newton, Page and Henderson and Pabis models. All thin layer drying models describe the experimental data well, but Page model is better than the other models on all various temperature with coefficients of determination (R2) range from 0.9908 to 0.9979, chi square range from 0.000212 to 0.000851 and RMSE range from 0.014307 to 0.0289458.

Elasticity-mediated nematiclike bacterial organization in model extracellular DNA matrix.

PubMed

Smalyukh, Ivan I; Butler, John; Shrout, Joshua D; Parsek, Matthew R; Wong, Gerard C L

2008-09-01

DNA is a common extracellular matrix component of bacterial biofilms. We find that bacteria can spontaneously order in a matrix of aligned concentrated DNA, in which rod-shaped cells of Pseudomonas aeruginosa follow the orientation of extended DNA chains. The alignment of bacteria is ensured by elasticity and liquid crystalline properties of the DNA matrix. These findings show how behavior of planktonic bacteria may be modified in extracellular polymeric substances of biofilms and illustrate the potential of using complex fluids to manipulate embedded nanosized and microsized active particles.

O Antigen Modulates Insect Vector Acquisition of the Bacterial Plant Pathogen Xylella fastidiosa

PubMed Central

Rapicavoli, Jeannette N.; Kinsinger, Nichola; Perring, Thomas M.; Backus, Elaine A.; Shugart, Holly J.; Walker, Sharon

2015-01-01

Hemipteran insect vectors transmit the majority of plant pathogens. Acquisition of pathogenic bacteria by these piercing/sucking insects requires intimate associations between the bacterial cells and insect surfaces. Lipopolysaccharide (LPS) is the predominant macromolecule displayed on the cell surface of Gram-negative bacteria and thus mediates bacterial interactions with the environment and potential hosts. We hypothesized that bacterial cell surface properties mediated by LPS would be important in modulating vector-pathogen interactions required for acquisition of the bacterial plant pathogen Xylella fastidiosa, the causative agent of Pierce's disease of grapevines. Utilizing a mutant that produces truncated O antigen (the terminal portion of the LPS molecule), we present results that link this LPS structural alteration to a significant decrease in the attachment of X. fastidiosa to blue-green sharpshooter foreguts. Scanning electron microscopy confirmed that this defect in initial attachment compromised subsequent biofilm formation within vector foreguts, thus impairing pathogen acquisition. We also establish a relationship between O antigen truncation and significant changes in the physiochemical properties of the cell, which in turn affect the dynamics of X. fastidiosa adhesion to the vector foregut. Lastly, we couple measurements of the physiochemical properties of the cell with hydrodynamic fluid shear rates to produce a Comsol model that predicts primary areas of bacterial colonization within blue-green sharpshooter foreguts, and we present experimental data that support the model. These results demonstrate that, in addition to reported protein adhesin-ligand interactions, O antigen is crucial for vector-pathogen interactions, specifically in the acquisition of this destructive agricultural pathogen. PMID:26386068

Semiquantitative Performance and Mechanism Evaluation of Carbon Nanomaterials as Cathode Coatings for Microbial Fouling Reduction.

PubMed

Zhang, Qiaoying; Nghiem, Joanne; Silverberg, Gregory J; Vecitis, Chad D

2015-07-01

In this study, we examine bacterial attachment and survival on a titanium (Ti) cathode coated with various carbon nanomaterials (CNM): pristine carbon nanotubes (CNT), oxidized carbon nanotubes (O-CNT), oxidized-annealed carbon nanotubes (OA-CNT), carbon black (CB), and reduced graphene oxide (rGO). The carbon nanomaterials were dispersed in an isopropyl alcohol-Nafion solution and were then used to dip-coat a Ti substrate. Pseudomonas fluorescens was selected as the representative bacterium for environmental biofouling. Experiments in the absence of an electric potential indicate that increased nanoscale surface roughness and decreased hydrophobicity of the CNM coating decreased bacterial adhesion. The loss of bacterial viability on the noncharged CNM coatings ranged from 22% for CB to 67% for OA-CNT and was dependent on the CNM dimensions and surface chemistry. For electrochemical experiments, the total density and percentage of inactivation of the adherent bacteria were analyzed semiquantitatively as functions of electrode potential, current density, and hydrogen peroxide generation. Electrode potential and hydrogen peroxide generation were the dominant factors with regard to short-term (3-h) bacterial attachment and inactivation, respectively. Extended-time electrochemical experiments (12 h) indicated that in all cases, the density of total deposited bacteria increased almost linearly with time and that the rate of bacterial adhesion was decreased 8- to 10-fold when an electric potential was applied. In summary, this study provides a fundamental rationale for the selection of CNM as cathode coatings and electric potential to reduce microbial fouling. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Near-infrared surface-enhanced-Raman-scattering (SERS) mediated detection of single optically trapped bacterial spores

NASA Astrophysics Data System (ADS)

Alexander, Troy A.; Pellegrino, Paul M.; Gillespie, James B.

2003-08-01

A novel methodology has been developed for the investigation of bacterial spores. Specifically, this method has been used to probe the spore coat composition of two different Bacillus stearothermophilus variants. This technique may be useful in many applications; most notably, development of novel detection schemes toward potentially harmful bacteria. This method would also be useful as an ancillary environmental monitoring system where sterility is of importance (i.e., food preparation areas as well as invasive and minimally invasive medical applications). This unique detection scheme is based on the near-infrared (NIR) Surface-Enhanced-Raman-Scattering (SERS) from single, optically trapped, bacterial spores. The SERS spectra of bacterial spores in aqueous media have been measured using SERS substrates based on ~60-nm diameter gold colloids bound to 3-Aminopropyltriethoxysilane derivatized glass. The light from a 787-nm laser diode was used to trap/manipulate as well as simultaneously excite the SERS of an individual bacterial spore. The collected SERS spectra were examined for uniqueness and the applicability of this technique for the strain discrimination of Bacillus stearothermophilus spores. Comparison of normal Raman and SERS spectra reveal not only an enhancement of the normal Raman spectral features but also the appearance of spectral features absent in the normal Raman spectrum.

Near-infrared Surface-Enhanced-Raman-Scattering (SERS) mediated discrimination of single optically trapped bacterial spores

NASA Astrophysics Data System (ADS)

Alexander, Troy A.; Pellegrino, Paul M.; Gillespie, James B.

2004-03-01

A novel methodology has been developed for the investigation of bacterial spores. Specifically, this method has been used to probe the spore coat composition of two different Bacillus stearothermophilus variants. This technique may be useful in many applications; most notably, development of novel detection schemes toward potentially harmful bacteria. This method would also be useful as an ancillary environmental monitoring system where sterility is of importance (i.e., food preparation areas as well as invasive and minimally invasive medical applications). This unique detection scheme is based on the near-infrared (NIR) Surface-Enhanced-Raman- Scattering (SERS) from single, optically trapped, bacterial spores. The SERS spectra of bacterial spores in aqueous media have been measured using SERS substrates based on ~60-nm diameter gold colloids bound to 3-Aminopropyltriethoxysilane derivatized glass. The light from a 787-nm laser diode was used to trap/manipulate as well as simultaneously excite the SERS of an individual bacterial spore. The collected SERS spectra were examined for uniqueness and the applicability of this technique for the strain discrimination of Bacillus stearothermophilus spores. Comparison of normal Raman and SERS spectra reveal not only an enhancement of the normal Raman spectral features but also the appearance of spectral features absent in the normal Raman spectrum.

Creation and formation mechanism of new carbon phases constructed by amorphous carbon

NASA Astrophysics Data System (ADS)

Yao, Mingguang; Cui, Wen; Liu, Bingbing

Our recent effort is focusing on the creation of new hard/superhard carbon phases constructed by disordered carbons or amorphous carbon clusters under high pressure. We showed that the pressure-induced amorphous hard carbon clusters from collapsed fullerenes can be used as building blocks (BBs) for constructing novel carbon structures. This new strategy has been verified by compressing a series of intercalated fullerides, pre-designed by selecting various dopants with special features. We demonstrate that the boundaries of the amorphous BBs are mediated by intercalated dopants and several new superhard materials have been prepared. We also found that the dopant-mediated BBs can be arranged in either ordered or disordered structures, both of which can be hard enough to indent the diamond anvils. The hardening mechanisms of the new phases have also been discussed. For the glassy carbon (GC) constructructed by disordered fullerene-like nanosized fragments, we also found that these disordered fragments can bond and the compressed GC transformed into a transparent superhard phase. Such pressure-induced transformation has been discovered to be driven by a novel mechanism (unpublished). By understanding the mechanisms we can clarify the controversial results on glassy carbon reported recently. The authors would like to thank the financial support from the National Natural Science Foundation of China (No. 11474121, 51320105007).

Aspect ratio has no effect on genotoxicity of multi-wall carbon nanotubes.

PubMed

Kim, Jin Sik; Lee, Kyu; Lee, Young Hee; Cho, Hyun Sun; Kim, Ki Heon; Choi, Kyung Hee; Lee, Sang Hee; Song, Kyung Seuk; Kang, Chang Soo; Yu, Il Je

2011-07-01

Carbon nanotubes (CNTs) have specific physico-chemical and electrical properties that are useful for telecommunications, medicine, materials, manufacturing processes and the environmental and energy sectors. Yet, despite their many advantages, it is also important to determine whether CNTs may represent a hazard to the environment and human health. Like asbestos, the aspect ratio (length:diameter) and metal components of CNTs are known to have an effect on the toxicity of carbon nanotubes. Thus, to evaluate the toxic potential of CNTs in relation to their aspect ratio and metal contamination, in vivo and in vitro genotoxicity tests were conducted using high-aspect-ratio (diameter: 10-15 nm, length: ~10 μm) and low-aspect-ratio multi-wall carbon nanotubes (MWCNTs, diameter: 10-15 nm, length: ~150 nm) according to OECD test guidelines 471 (bacterial reverse mutation test), 473 (in vitro chromosome aberration test), and 474 (in vivo micronuclei test) with a good laboratory practice system. To determine the treatment concentration for all the tests, a solubility and dispersive test was performed, and a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) solution found to be more suitable than distilled water. Neither the high- nor the low-aspect-ratio MWCNTs induced any genotoxicity in a bacterial reverse mutation test (~1,000 μg/plate), in vitro chromosome aberration test (without S9: ~6.25 μg/ml, with S9: ~50 μg/ml), or in vivo micronuclei test (~50 mg/kg). However, the high-aspect-ratio MWCNTs were found to be more toxic than the low-aspect-ratio MWCNTs. Thus, while high-aspect-ratio MWCNTs do not induce direct genotoxicity or metabolic activation-mediated genotoxicity, genotoxicity could still be induced indirectly through oxidative stress or inflammation.

Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances.

PubMed

Zhou, Xingang; Wang, Zhilin; Jia, Huiting; Li, Li; Wu, Fengzhi

2018-01-01

Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA) system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA , nirS , and nirK genes. Results showed that 1-2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity ( P < 0.05). Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile ( P < 0.001). At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria , Planctomycetes , and Cyanobacteria , the first cropping of JA with Actinobacteria , the second cropping of JA with Acidobacteria , Armatimonadetes , Gemmatimonadetes , and Proteobacteria . At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO terms

Millennial-scale ocean acidification and late Quaternary decline of cryptic bacterial crusts in tropical reefs.

PubMed

Riding, R; Liang, L; Braga, J C

2014-09-01

Ocean acidification by atmospheric carbon dioxide has increased almost continuously since the last glacial maximum (LGM), 21,000 years ago. It is expected to impair tropical reef development, but effects on reefs at the present day and in the recent past have proved difficult to evaluate. We present evidence that acidification has already significantly reduced the formation of calcified bacterial crusts in tropical reefs. Unlike major reef builders such as coralline algae and corals that more closely control their calcification, bacterial calcification is very sensitive to ambient changes in carbonate chemistry. Bacterial crusts in reef cavities have declined in thickness over the past 14,000 years with largest reduction occurring 12,000-10,000 years ago. We interpret this as an early effect of deglacial ocean acidification on reef calcification and infer that similar crusts were likely to have been thicker when seawater carbonate saturation was increased during earlier glacial intervals, and thinner during interglacials. These changes in crust thickness could have substantially affected reef development over glacial cycles, as rigid crusts significantly strengthen framework and their reduction would have increased the susceptibility of reefs to biological and physical erosion. Bacterial crust decline reveals previously unrecognized millennial-scale acidification effects on tropical reefs. This directs attention to the role of crusts in reef formation and the ability of bioinduced calcification to reflect changes in seawater chemistry. It also provides a long-term context for assessing anticipated anthropogenic effects. © 2014 John Wiley & Sons Ltd.

Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest

PubMed Central

Xiang, Xingjia; Shi, Yu; Yang, Jian; Kong, Jianjian; Lin, Xiangui; Zhang, Huayong; Zeng, Jun; Chu, Haiyan

2014-01-01

Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20–100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties. PMID:24452061

Crystal structure of the Haemophilus influenzae Hap adhesin reveals an intercellular oligomerization mechanism for bacterial aggregation

PubMed Central

Meng, Guoyu; Spahich, Nicole; Kenjale, Roma; Waksman, Gabriel; St Geme, Joseph W

2011-01-01

Bacterial biofilms are complex microbial communities that are common in nature and are being recognized increasingly as an important determinant of bacterial virulence. However, the structural determinants of bacterial aggregation and eventual biofilm formation have been poorly defined. In Gram-negative bacteria, a major subgroup of extracellular proteins called self-associating autotransporters (SAATs) can mediate cell–cell adhesion and facilitate biofilm formation. In this study, we used the Haemophilus influenzae Hap autotransporter as a prototype SAAT to understand how bacteria associate with each other. The crystal structure of the H. influenzae HapS passenger domain (harbouring the SAAT domain) was determined to 2.2 Å by X-ray crystallography, revealing an unprecedented intercellular oligomerization mechanism for cell–cell interaction. The C-terminal SAAT domain folds into a triangular-prism-like structure that can mediate Hap–Hap dimerization and higher degrees of multimerization through its F1–F2 edge and F2 face. The intercellular multimerization can give rise to massive buried surfaces that are required for overcoming the repulsive force between cells, leading to bacterial cell–cell interaction and formation of complex microcolonies. PMID:21841773

S1PR3 Signaling Drives Bacterial Killing and Is Required for Survival in Bacterial Sepsis.

PubMed

Hou, JinChao; Chen, QiXing; Wu, XiaoLiang; Zhao, DongYan; Reuveni, Hadas; Licht, Tamar; Xu, MengLong; Hu, Hu; Hoeft, Andreas; Ben-Sasson, Shmuel A; Shu, Qiang; Fang, XiangMing

2017-12-15

Efficient elimination of pathogenic bacteria is a critical determinant in the outcome of sepsis. Sphingosine-1-phosphate receptor 3 (S1PR3) mediates multiple aspects of the inflammatory response during sepsis, but whether S1PR3 signaling is necessary for eliminating the invading pathogens remains unknown. To investigate the role of S1PR3 in antibacterial immunity during sepsis. Loss- and gain-of-function experiments were performed using cell and murine models. S1PR3 levels were determined in patients with sepsis and healthy volunteers. S1PR3 protein levels were up-regulated in macrophages upon bacterial stimulation. S1pr3 -/- mice showed increased mortality and increased bacterial burden in multiple models of sepsis. The transfer of wild-type bone marrow-derived macrophages rescued S1pr3 -/- mice from lethal sepsis. S1PR3-overexpressing macrophages further ameliorated the mortality rate of sepsis. Loss of S1PR3 led to markedly decreased bacterial killing in macrophages. Enhancing endogenous S1PR3 activity using a peptide agonist potentiated the macrophage bactericidal function and improved survival rates in multiple models of sepsis. Mechanically, the reactive oxygen species levels were decreased and phagosome maturation was delayed in S1pr3 -/- macrophages due to impaired recruitment of vacuolar protein-sorting 34 to the phagosomes. In addition, S1RP3 expression levels were elevated in monocytes from patients with sepsis. Higher levels of monocytic S1PR3 were associated with efficient intracellular bactericidal activity, better immune status, and preferable outcomes. S1PR3 signaling drives bacterial killing and is essential for survival in bacterial sepsis. Interventions targeting S1PR3 signaling could have translational implications for manipulating the innate immune response to combat pathogens.

Bacterial chemoreceptors: high-performance signaling in networked arrays.

PubMed

Hazelbauer, Gerald L; Falke, Joseph J; Parkinson, John S

2008-01-01

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on-off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device.

Bacterial chemoreceptors: high-performance signaling in networked arrays

PubMed Central

Hazelbauer, Gerald L.; Falke, Joseph J.; Parkinson, John S.

2010-01-01

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on–off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device. PMID:18165013

Study of Bacterial Samples Using Laser Induced Breakdown Spectroscopy

NASA Astrophysics Data System (ADS)

W, A. Farooq; M, Atif; W, Tawfik; M, S. Alsalhi; Z, A. Alahmed; M, Sarfraz; J, P. Singh

2014-12-01

Laser-induced breakdown spectroscopy (LIBS) technique has been applied to investigate two different types of bacteria, Escherichia coli (B1) and Micrococcus luteus (B2) deposited on glass slides using Spectrolaser 7000. LIBS spectra were analyzed using spectrolaser software. LIBS spectrum of glass substrate was compared with bacteria spectra. Ca, Mg, Na, K, P, S, Cl, Fe, Al, Mn, Cu, C, H and CN-band appeared in bacterial samples in air. Two carbon lines at 193.02 nm, 247.88 nm and one hydrogen line at 656.28 nm with intensity ratios of 1.9, 1.83 and 1.53 appeared in bacterial samples B1 and B2 respectively. Carbon and hydrogen are the important components of the bio-samples like bacteria and other cancer cells. Investigation on LIBS spectra of the samples in He and Ar atmospheres is also presented. Ni lines appeared only in B2 sample in Ar atmosphere. From the present experimental results we are able to show that LIBS technique has a potential in the identification and discrimination of different types of bacteria.

Channel-Forming Bacterial Toxins in Biosensing and Macromolecule Delivery

PubMed Central

Gurnev, Philip A.; Nestorovich, Ekaterina M.

2014-01-01

To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on “Intracellular Traffic and Transport of Bacterial Protein Toxins”, reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their “second life” in a variety of developing medical and technological applications. PMID:25153255

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level

PubMed Central

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-01-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial–microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner. PMID:28742069

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

PubMed

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

Brood size modifications affect plumage bacterial assemblages of European starlings.

PubMed

Lucas, Françoise S; Moureau, Benoit; Jourdie, Violaine; Heeb, Philipp

2005-02-01

During reproduction, birds face trade-offs between time and energy devoted to parental effort and traits associated with self-maintenance. We manipulated brood sizes to investigate the effects of such trade-offs on feather bacterial densities and the structure of bacterial assemblages on feathers in adult European starlings, Sturnus vulgaris, and in vitro feather degradation. As predicted by a trade-off between parental effort and self-maintenance, we found that birds with enlarged broods had more free-living bacteria on their feathers than birds with reduced broods. Furthermore, we found a significant interaction between brood manipulation and original brood size on free-living bacterial densities suggesting that the trade-off is mediated by the adults' initial reproductive investment. In contrast, brood size manipulations had no significant effect on densities of attached bacteria. Using ribosomal intergenic spacer analysis (RISA), we demonstrated that brood manipulations significantly modified the structure (band pattern) of feather-degrading bacterial assemblages, but had no significant effect on their richness (number of bands) or the in vitro feather degradation. In vitro feather degradation varied in relation to the premanipulation brood size and positively with the richness of the feather degrading bacterial community. Besides brood manipulation effect, we found that ecological factors and individual traits, such as the age, the nest location or the capture date, shaped bacterial assemblages and feather degradation capacities.

Origins of carbonate spherulites: Implications for Brazilian Aptian pre-salt reservoir

NASA Astrophysics Data System (ADS)

Chafetz, Henry; Barth, Jennifer; Cook, Megan; Guo, Xuan; Zhou, Jie

2018-03-01

Spherulites, spherical to elliptical allochems composed of crystals radiating from a common core, investigated from a variety of depositional settings, e.g., hot springs, ambient water temperature geyser, tufa, and caliche, are all composed of a fine-grained nucleus made-up of carbonate encrusted bacterial bodies, biofilms, and/or EPS and surrounded by a cortex of radiating crystals of either aragonite or calcite. The microbes and their by-products in the nucleus induced the precipitation of carbonate, overcoming the inhibition to initiate crystal formation. The enveloping radiating crystals comprising aragonitic cortices tended to grow abiotically producing well-formed euhedral crystals with a paucity of included bacterial fossils. Whereas those cortical crystals made-up of calcite commonly contained bacterial fossils, indicating that the bacterial colonies contributed to the calcitic cortical crystal precipitation. Similar spherulites form a thick, widespread accumulation in the Aptian Pre-Salt lacustrine deposits in the Campos Basin, offshore Brazil. As with the travertine, tufa, and caliche spherulites, the Pre-Salt spherulites most likely initiated carbonate precipitation around bacterial colonies and/or their bioproducts, probably while afloat in a lacustrine water column before settling to the water-sediment interface. Absence of inter-spherulite sediment and the spherulite-to-spherulite compaction indicate that cortical crystal growth continued while the spherulites were at the sediment-water interface rather than displacively within a sediment.

Biofuel components change the ecology of bacterial volatile petroleum hydrocarbon degradation in aerobic sandy soil.

PubMed

Elazhari-Ali, Abdulmagid; Singh, Arvind K; Davenport, Russell J; Head, Ian M; Werner, David

2013-02-01

We tested the hypothesis that the biodegradation of volatile petroleum hydrocarbons (VPHs) in aerobic sandy soil is affected by the blending with 10 percent ethanol (E10) or 20 percent biodiesel (B20). When inorganic nutrients were scarce, competition between biofuel and VPH degraders temporarily slowed monoaromatic hydrocarbon degradation. Ethanol had a bigger impact than biodiesel, reflecting the relative ease of ethanol compared to methyl ester biodegradation. Denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA genes revealed that each fuel mixture selected for a distinct bacterial community, each dominated by Pseudomonas spp. Despite lasting impacts on soil bacterial ecology, the overall effects on VHP biodegradation were minor, and average biomass yields were comparable between fuel types, ranging from 0.40 ± 0.16 to 0.51 ± 0.22 g of biomass carbon per gram of fuel carbon degraded. Inorganic nutrient availability had a greater impact on petroleum hydrocarbon biodegradation than fuel composition. Copyright © 2012 Elsevier Ltd. All rights reserved.

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions.

PubMed

Szabó, Attila; Korponai, Kristóf; Kerepesi, Csaba; Somogyi, Boglárka; Vörös, Lajos; Bartha, Dániel; Márialigeti, Károly; Felföldi, Tamás

2017-05-01

Soda pans of the Pannonian steppe are unique environments regarding their physical and chemical characteristics: shallowness, high turbidity, intermittent character, alkaline pH, polyhumic organic carbon concentration, hypertrophic condition, moderately high salinity, sodium and carbonate ion dominance. The pans are highly productive environments with picophytoplankton predominance. Little is known about the planktonic bacterial communities inhabiting these aquatic habitats; therefore, amplicon sequencing and shotgun metagenomics were applied to reveal their composition and functional properties. Results showed a taxonomically complex bacterial community which was distinct from other soda lakes regarding its composition, e.g. the dominance of class Alphaproteobacteria was observed within phylum Proteobacteria. The shotgun metagenomic analysis revealed several functional gene components related to the harsh and at the same time hypertrophic environmental conditions, e.g. proteins involved in stress response, transport and hydrolase systems targeting phytoplankton-derived organic matter. This is the first detailed report on the indigenous planktonic bacterial communities coping with the multiple extreme conditions present in the unique soda pans of the Pannonian steppe.

Role of Pore-Forming Toxins in Bacterial Infectious Diseases

PubMed Central

Los, Ferdinand C. O.; Randis, Tara M.

2013-01-01

SUMMARY Pore-forming toxins (PFTs) are the most common bacterial cytotoxic proteins and are required for virulence in a large number of important pathogens, including Streptococcus pneumoniae, group A and B streptococci, Staphylococcus aureus, Escherichia coli, and Mycobacterium tuberculosis. PFTs generally disrupt host cell membranes, but they can have additional effects independent of pore formation. Substantial effort has been devoted to understanding the molecular mechanisms underlying the functions of certain model PFTs. Likewise, specific host pathways mediating survival and immune responses in the face of toxin-mediated cellular damage have been delineated. However, less is known about the overall functions of PFTs during infection in vivo. This review focuses on common themes in the area of PFT biology, with an emphasis on studies addressing the roles of PFTs in in vivo and ex vivo models of colonization or infection. Common functions of PFTs include disruption of epithelial barrier function and evasion of host immune responses, which contribute to bacterial growth and spreading. The widespread nature of PFTs make this group of toxins an attractive target for the development of new virulence-targeted therapies that may have broad activity against human pathogens. PMID:23699254

Conservation of ornamental stone by Myxococcus xanthus-induced carbonate biomineralization.

PubMed

Rodriguez-Navarro, Carlos; Rodriguez-Gallego, Manuel; Ben Chekroun, Koutar; Gonzalez-Muñoz, Maria Teresa

2003-04-01

Increasing environmental pollution in urban areas has been endangering the survival of carbonate stones in monuments and statuary for many decades. Numerous conservation treatments have been applied for the protection and consolidation of these works of art. Most of them, however, either release dangerous gases during curing or show very little efficacy. Bacterially induced carbonate mineralization has been proposed as a novel and environmentally friendly strategy for the conservation of deteriorated ornamental stone. However, the method appeared to display insufficient consolidation and plugging of pores. Here we report that Myxococcus xanthus-induced calcium carbonate precipitation efficiently protects and consolidates porous ornamental limestone. The newly formed carbonate cements calcite grains by depositing on the walls of the pores without plugging them. Sonication tests demonstrate that these new carbonate crystals are strongly attached to the substratum, mostly due to epitaxial growth on preexisting calcite grains. The new crystals are more stress resistant than the calcite grains of the original stone because they are organic-inorganic composites. Variations in the phosphate concentrations of the culture medium lead to changes in local pH and bacterial productivity. These affect the structure of the new cement and the type of precipitated CaCO(3) polymorph (vaterite or calcite). The manipulation of culture medium composition creates new ways of controlling bacterial biomineralization that in the future could be applied to the conservation of ornamental stone.

Conservation of Ornamental Stone by Myxococcus xanthus-Induced Carbonate Biomineralization

PubMed Central

Rodriguez-Navarro, Carlos; Rodriguez-Gallego, Manuel; Ben Chekroun, Koutar; Gonzalez-Muñoz, Maria Teresa

2003-01-01

Increasing environmental pollution in urban areas has been endangering the survival of carbonate stones in monuments and statuary for many decades. Numerous conservation treatments have been applied for the protection and consolidation of these works of art. Most of them, however, either release dangerous gases during curing or show very little efficacy. Bacterially induced carbonate mineralization has been proposed as a novel and environmentally friendly strategy for the conservation of deteriorated ornamental stone. However, the method appeared to display insufficient consolidation and plugging of pores. Here we report that Myxococcus xanthus-induced calcium carbonate precipitation efficiently protects and consolidates porous ornamental limestone. The newly formed carbonate cements calcite grains by depositing on the walls of the pores without plugging them. Sonication tests demonstrate that these new carbonate crystals are strongly attached to the substratum, mostly due to epitaxial growth on preexisting calcite grains. The new crystals are more stress resistant than the calcite grains of the original stone because they are organic-inorganic composites. Variations in the phosphate concentrations of the culture medium lead to changes in local pH and bacterial productivity. These affect the structure of the new cement and the type of precipitated CaCO3 polymorph (vaterite or calcite). The manipulation of culture medium composition creates new ways of controlling bacterial biomineralization that in the future could be applied to the conservation of ornamental stone. PMID:12676699

Bacterial community evolutions driven by organic matter and powder activated carbon in simultaneous anammox and denitrification (SAD) process.

PubMed

Ge, Cheng-Hao; Sun, Na; Kang, Qi; Ren, Long-Fei; Ahmad, Hafiz Adeel; Ni, Shou-Qing; Wang, Zhibin

2018-03-01

A distinct shift of bacterial community driven by organic matter (OM) and powder activated carbon (PAC) was discovered in the simultaneous anammox and denitrification (SAD) process which was operated in an anti-fouling submerged anaerobic membrane bio-reactor. Based on anammox performance, optimal OM dose (50 mg/L) was advised to start up SAD process successfully. The results of qPCR and high throughput sequencing analysis indicated that OM played a key role in microbial community evolutions, impelling denitrifiers to challenge anammox's dominance. The addition of PAC not only mitigated the membrane fouling, but also stimulated the enrichment of denitrifiers, accounting for the predominant phylum changing from Planctomycetes to Proteobacteria in SAD process. Functional genes forecasts based on KEGG database and COG database showed that the expressions of full denitrification functional genes were highly promoted in R C , which demonstrated the enhanced full denitrification pathway driven by OM and PAC under low COD/N value (0.11). Copyright © 2017 Elsevier Ltd. All rights reserved.

Sample Dilution and Bacterial Community Composition Influence Empirical Leucine-to-Carbon Conversion Factors in Surface Waters of the World's Oceans

PubMed Central

Hernando-Morales, Víctor; Cornejo-Castillo, Francisco M.; Alonso-Sáez, Laura; Sarmento, Hugo; Valencia-Vila, Joaquín; Serrano Catalá, Teresa; Hernández-Ruiz, Marta; Varela, Marta M.; Ferrera, Isabel; Gutiérrez Morán, Xosé Anxelu; Gasol, Josep M.

2015-01-01

The transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu−1 and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean. PMID:26407885

Chemotaxis towards autoinducer 2 mediates autoaggregation in Escherichia coli

PubMed Central

Laganenka, Leanid; Colin, Remy; Sourjik, Victor

2016-01-01

Bacteria communicate by producing and sensing extracellular signal molecules called autoinducers. Such intercellular signalling, known as quorum sensing, allows bacteria to coordinate and synchronize behavioural responses at high cell densities. Autoinducer 2 (AI-2) is the only known quorum-sensing molecule produced by Escherichia coli but its physiological role remains elusive, although it is known to regulate biofilm formation and virulence in other bacterial species. Here we show that chemotaxis towards self-produced AI-2 can mediate collective behaviour—autoaggregation—of E. coli. Autoaggregation requires motility and is strongly enhanced by chemotaxis to AI-2 at physiological cell densities. These effects are observed regardless whether cell–cell interactions under particular growth conditions are mediated by the major E. coli adhesin (antigen 43) or by curli fibres. Furthermore, AI-2-dependent autoaggregation enhances bacterial stress resistance and promotes biofilm formation. PMID:27687245

Malate-Mediated Carbon Catabolite Repression in Bacillus subtilis Involves the HPrK/CcpA Pathway ▿ §

PubMed Central

Meyer, Frederik M.; Jules, Matthieu; Mehne, Felix M. P.; Le Coq, Dominique; Landmann, Jens J.; Görke, Boris; Aymerich, Stéphane; Stülke, Jörg

2011-01-01

Most organisms can choose their preferred carbon source from a mixture of nutrients. This process is called carbon catabolite repression. The Gram-positive bacterium Bacillus subtilis uses glucose as the preferred source of carbon and energy. Glucose-mediated catabolite repression is caused by binding of the CcpA transcription factor to the promoter regions of catabolic operons. CcpA binds DNA upon interaction with its cofactors HPr(Ser-P) and Crh(Ser-P). The formation of the cofactors is catalyzed by the metabolite-activated HPr kinase/phosphorylase. Recently, it has been shown that malate is a second preferred carbon source for B. subtilis that also causes catabolite repression. In this work, we addressed the mechanism by which malate causes catabolite repression. Genetic analyses revealed that malate-dependent catabolite repression requires CcpA and its cofactors. Moreover, we demonstrate that HPr(Ser-P) is present in malate-grown cells and that CcpA and HPr interact in vivo in the presence of glucose or malate but not in the absence of a repressing carbon source. The formation of the cofactor HPr(Ser-P) could be attributed to the concentrations of ATP and fructose 1,6-bisphosphate in cells growing with malate. Both metabolites are available at concentrations that are sufficient to stimulate HPr kinase activity. The adaptation of cells to environmental changes requires dynamic metabolic and regulatory adjustments. The repression strength of target promoters was similar to that observed in steady-state growth conditions, although it took somewhat longer to reach the second steady-state of expression when cells were shifted to malate. PMID:22001508

Green synthesis of bacterial mediated anti-proliferative gold nanoparticles: inducing mitotic arrest (G2/M phase) and apoptosis (intrinsic pathway)

NASA Astrophysics Data System (ADS)

Ganesh Kumar, C.; Poornachandra, Y.; Chandrasekhar, Cheemalamarri

2015-11-01

The physiochemical and biological properties of microbial derived gold nanoparticles have potential applications in various biomedical domains as well as in cancer therapy. We have fabricated anti-proliferative bacterial mediated gold nanoparticles (b-Au NPs) using a culture supernatant of Streptomyces clavuligerus and later characterized them by UV-visible, TEM, DLS, XRD and FT-IR spectroscopic techniques. The capping agent responsible for the nanoparticle formation was characterized based on SDS-PAGE and MALDI-TOF-MS analyses. They were tested for anticancer activity in A549, HeLa and DU145 cell lines. The biocompatibility and non-toxic nature of the nanoparticles were tested on normal human lung cell line (MRC-5). The b-Au NPs induced the cell cycle arrest in G2/M phase and also inhibited the microtubule assembly in DU145 cells. Mechanistic studies, such as ROS, MMP, Cyt-c, GSH, caspases 9, 8 and 3 activation and the Annexin V-FITC staining, along with the above parameters tested provided sufficient evidence that the b-Au NPs induced apoptosis through the intrinsic pathway. The results supported the use of b-Au NPs for future therapeutic application in cancer therapy and other biomedical applications.The physiochemical and biological properties of microbial derived gold nanoparticles have potential applications in various biomedical domains as well as in cancer therapy. We have fabricated anti-proliferative bacterial mediated gold nanoparticles (b-Au NPs) using a culture supernatant of Streptomyces clavuligerus and later characterized them by UV-visible, TEM, DLS, XRD and FT-IR spectroscopic techniques. The capping agent responsible for the nanoparticle formation was characterized based on SDS-PAGE and MALDI-TOF-MS analyses. They were tested for anticancer activity in A549, HeLa and DU145 cell lines. The biocompatibility and non-toxic nature of the nanoparticles were tested on normal human lung cell line (MRC-5). The b-Au NPs induced the cell cycle arrest in G2

Loop-Mediated Isothermal Amplification of Specific Endoglucanase Gene Sequence for Detection of the Bacterial Wilt Pathogen Ralstonia solanacearum

PubMed Central

Pirc, Manca; Llop, Pablo; Ravnikar, Maja; Dreo, Tanja

2014-01-01

The increased globalization of crops production and processing industries also promotes the side-effects of more rapid and efficient spread of plant pathogens. To prevent the associated economic losses, and particularly those related to bacterial diseases where their management relies on removal of the infected material from production, simple, easy-to-perform, rapid and cost-effective tests are needed. Loop-mediated isothermal amplification (LAMP) assays that target 16S rRNA, fliC and egl genes were compared and evaluated as on-site applications. The assay with the best performance was that targeted to the egl gene, which shows high analytical specificity for diverse strains of the betaproteobacterium Ralstonia solanacearum, including its non-European and non-race 3 biovar 2 strains. The additional melting curve analysis provides confirmation of the test results. According to our extensive assessment, the egl LAMP assay requires minimum sample preparation (a few minutes of boiling) for the identification of pure cultures and ooze from symptomatic material, and it can also be used in a high-throughput format in the laboratory. This provides sensitive and reliable detection of R. solanacearum strains of different phylotypes. PMID:24763488

Influence of carbon steel grade on the initial attachment of bacteria and microbiologically influenced corrosion.

PubMed

Javed, M A; Neil, W C; Stoddart, P R; Wade, S A

2016-01-01

The influence of the composition and microstructure of different carbon steel grades on the initial attachment (≤ 60 min) of Escherichia coli and subsequent longer term (28 days) corrosion was investigated. The initial bacterial attachment increased with time on all grades of carbon steel. However, the rate and magnitude of bacterial attachment varied on the different steel grades and was significantly less on the steels with a higher pearlite phase content. The observed variations in the number of bacterial cells attached across different steel grades were significantly reduced by applying a fixed potential to the steel samples. Longer term immersion studies showed similar levels of biofilm formation on the surface of the different grades of carbon steel. The measured corrosion rates were significantly higher in biotic conditions compared to abiotic conditions and were found to be positively correlated with the pearlite phase content of the different grades of carbon steel coupons.

Incorporation of bacterial extracellular polysaccharide by black fly larvae (Simuliidae)

USGS Publications Warehouse

Couch, C.A.; Meyer, J.L.; Hall, R.O.

1996-01-01

Black fly larvae (Simulium) assimilated, with high efficiency (80-90%), bacterial extracellular polysaccharide (EPS) extracted from laboratory cultures of a pseudomonad isolated from the Ogeechee River. Incorporation was traced using 13C-labelled EPS offered to larvae as a coating on a mixture of 1-??m latex beads and kaolin particles. These EPS-coated particles were used to simulate natural particles, both living and dead. Solubility, protein, and nitrogen content of the EPS suggested it was a slime rather than a capsular polysaccharide. Glycosyl composition of the EPS was glucose and galactose in ?? and ?? linkages, with pyruvate, succinate, and possibly malonate constituent groups. To evaluate the incorporation of C derived from protein associated with the EPS matrix, feeding experiments were conducted using EPS with and without proteins extracted. Black fly larvae incorporated 7.2 ??g EPS C larva-1 d-1 from EPS that did not have proteins extracted, and 19.5 ??g EPS C larva-1 d-1 from EPS with proteins extracted. Carbon in protein that is typically associated with EPS was not solely or selectively incorporated. EPS incorporation rates are similar to rates of cellular bacterial carbon incorporation previously estimated for Ogeechee River black fly larvae. If EPS is generally available as a food resource, the importance of bacteria in detrital food webs may be underestimated by studies that examine only the consumption of bacterial cells.

A phosphine mediated sequential annulation process of 2-tosylaminochalcones with MBH carbonates to construct functionalized aza-benzobicyclo[4.3.0] derivatives.

PubMed

Zhang, Qinglong; Zhu, Yannan; Jin, Hongxing; Huang, You

2017-04-04

A novel phosphine mediated sequential annulation process to construct functionalized aza-benzobicyclo[4.3.0] derivatives has been developed involving a one-pot sequential catalytic and stoichiometric process, which generates a series of benzobicyclo[4.3.0] compounds containing one quaternary center with up to 94% yield and 20 : 1 dr value. In this reaction, MBH carbonates act as 1,2,3-C 3 synthons.

Molecular mechanisms of cell-cell spread of intracellular bacterial pathogens.

PubMed

Ireton, Keith

2013-07-17

Several bacterial pathogens, including Listeria monocytogenes, Shigella flexneri and Rickettsia spp., have evolved mechanisms to actively spread within human tissues. Spreading is initiated by the pathogen-induced recruitment of host filamentous (F)-actin. F-actin forms a tail behind the microbe, propelling it through the cytoplasm. The motile pathogen then encounters the host plasma membrane, forming a bacterium-containing protrusion that is engulfed by an adjacent cell. Over the past two decades, much progress has been made in elucidating mechanisms of F-actin tail formation. Listeria and Shigella produce tails of branched actin filaments by subverting the host Arp2/3 complex. By contrast, Rickettsia forms tails with linear actin filaments through a bacterial mimic of eukaryotic formins. Compared with F-actin tail formation, mechanisms controlling bacterial protrusions are less well understood. However, recent findings have highlighted the importance of pathogen manipulation of host cell-cell junctions in spread. Listeria produces a soluble protein that enhances bacterial protrusions by perturbing tight junctions. Shigella protrusions are engulfed through a clathrin-mediated pathway at 'tricellular junctions'--specialized membrane regions at the intersection of three epithelial cells. This review summarizes key past findings in pathogen spread, and focuses on recent developments in actin-based motility and the formation and internalization of bacterial protrusions.

Immobilization of a mediator onto carbon cloth electrode and employment of the modified electrode to an electroenzymatic bioreactor.

PubMed

Jeong, Eun-Seon; Sathishkumar, Muthuswamy; Jayabalan, Rasu; Jeong, Su-Hyeon; Park, Song-Yie; Mun, Sung-Phil; Yun, Sei-Eok

2012-10-01

5,5'-Dithiobis(2-nitrobenzoic acid) (DTNB) was selected as an electron transfer mediator and was covalently immobilized onto high porosity carbon cloth to employ as a working electrode in an electrochemical NAD(+)-regeneration process, which was coupled to an enzymatic reaction. The voltammetric behavior of DTNB attached to carbon cloth resembled that of DTNB in buffered aqueous solution, and the electrocatalytic anodic current grew continuously upon addition of NADH at different concentrations, indicating that DTNB is immobilized to carbon cloth effectively and the immobilized DTNB is active as a soluble one. The bioelectrocatalytic NAD+ regeneration was coupled to the conversion of L-glutamate into alpha-ketoglutarate by L-glutamate dehydrogenase within the same microreactor. The conversion at 3 mM monosodium glutamate was very rapid, up to 12 h, to result in 90%, and then slow up to 24 h, showing 94%, followed by slight decrease. Low conversion was shown when substrate concentration exceeding 4 mM was tested, suggesting that L-glutamate dehydrogenase is inhibited by alpha-ketoglutarate. However, our electrochemical NAD+ regeneration procedure looks advantageous over the enzymatic procedure using NADH oxidase, from the viewpoint of reaction time to completion.

Increasing the Size of the Microbial Biomass Altered Bacterial Community Structure which Enhances Plant Phosphorus Uptake

PubMed Central

Shen, Pu; Murphy, Daniel Vaughan; George, Suman J.; Lapis-Gaza, Hazel; Xu, Minggang

2016-01-01

Agricultural production can be limited by low phosphorus (P) availability, with soil P being constrained by sorption and precipitation reactions making it less available for plant uptake. There are strong links between carbon (C) and nitrogen (N) availability and P cycling within soil P pools, with microorganisms being an integral component of soil P cycling mediating the availability of P to plants. Here we tested a conceptual model that proposes (i) the addition of readily-available organic substrates would increase the size of the microbial biomass thus exhausting the pool of easily-available P and (ii) this would cause the microbial biomass to access P from more recalcitrant pools. In this model it is hypothesised that the size of the microbial population is regulating access to less available P rather than the diversity of organisms contained within this biomass. To test this hypothesis we added mixtures of simple organic compounds that reflect typical root exudates at different C:N ratios to a soil microcosm experiment and assessed changes in soil P pools, microbial biomass and bacterial diversity measures. We report that low C:N ratio (C:N = 12.5:1) artificial root exudates increased the size of the microbial biomass while high C:N ratio (C:N = 50:1) artificial root exudates did not result in a similar increase in microbial biomass. Interestingly, addition of the root exudates did not alter bacterial diversity (measured via univariate diversity indices) but did alter bacterial community structure. Where C, N and P supply was sufficient to support plant growth the increase observed in microbial biomass occurred with a concurrent increase in plant yield. PMID:27893833

Vertical stratification of bacterial communities driven by multiple environmental factors in the waters (0-5000 m) off the Galician coast (NW Iberian margin)

NASA Astrophysics Data System (ADS)

Dobal-Amador, Vladimir; Nieto-Cid, Mar; Guerrero-Feijoo, Elisa; Hernando-Morales, Victor; Teira, Eva; Varela-Rozados, Marta M.

2016-08-01

The processes mediated by microbial planktonic communities occur along the entire water column, yet the microbial activity and composition have been studied mainly in surface waters. This research examined the vertical variation in bacterial abundance, activity and community composition and structure from surface down to 5000 m depth following a longitudinal transect off the Galician coast (NW Iberian margin, from 43°N, 9°W to 43°N, 15°W). Community activity and composition changed with depth. The leucine incorporation rates decreased from the euphotic layer to the bathypelagic waters by three orders of magnitude, whereas prokaryotic abundance decreased only by one order of magnitude. The relative abundance of SAR11 and Alteromonas, determined by catalyzed reported deposition fluorescence in situ hybridization (CARD-FISH), decreased with depth. Meanwhile, the contribution of SAR 202 and SAR324 was significantly higher in the deeper layers (i.e. NEADW, North East Atlantic Deep Water and LDW, Lower Deep Water) than in the euphotic zone. Bacterial community structure, assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA), was depth-specific. A distance based linear model (DistLM) revealed that the variability found in bacterial community structure was mainly explained by temperature nitrate, phosphate, dissolved organic matter (DOM) fluorescence, prokaryotic abundance, leucine incorporation and to a lesser extent salinity, oxygen, CDOM absorbance and dissolved organic carbon concentration. Our results displayed a bacterial community structure shaped not only by depth-related physicochemical features but also by DOM quality, indicating that different prokaryotic taxa have the potential to metabolize particular DOM sources.

Mechanistic insights into the allosteric regulation of bacterial ADP-glucose pyrophosphorylases

PubMed Central

Comino, Natalia; Cifuente, Javier O.; Marina, Alberto; Orrantia, Ane; Eguskiza, Ander; Guerin, Marcelo E.

2017-01-01

ADP-glucose pyrophosphorylase (AGPase) controls bacterial glycogen and plant starch biosynthetic pathways, the most common carbon storage polysaccharides in nature. AGPase activity is allosterically regulated by a series of metabolites in the energetic flux within the cell. Very recently, we reported the first crystal structures of the paradigmatic AGPase from Escherichia coli (EcAGPase) in complex with its preferred physiological negative and positive allosteric regulators, adenosine 5′-monophosphate (AMP) and fructose 1,6-bisphosphate (FBP), respectively. However, understanding the molecular mechanism by which AMP and FBP allosterically modulates EcAGPase enzymatic activity still remains enigmatic. Here we found that single point mutations of key residues in the AMP-binding site decrease its inhibitory effect but also clearly abolish the overall AMP-mediated stabilization effect in wild-type EcAGPase. Single point mutations of key residues for FBP binding did not revert the AMP-mediated stabilization. Strikingly, an EcAGPase-R130A mutant displayed a dramatic increase in activity when compared with wild-type EcAGPase, and this increase correlated with a significant increment of glycogen content in vivo. The crystal structure of EcAGPase-R130A revealed unprecedented conformational changes in structural elements involved in the allosteric signal transmission. Altogether, we propose a model in which the positive and negative energy reporters regulate AGPase catalytic activity via intra- and interprotomer cross-talk, with a “sensory motif” and two loops, RL1 and RL2, flanking the ATP-binding site playing a significant role. The information reported herein provides exciting possibilities for industrial/biotechnological applications. PMID:28223362

Effect of redox conditions on bacterial and fungal biomass and carbon dioxide production in Louisiana coastal swamp forest sediment.

PubMed

Seo, Dong Cheol; DeLaune, Ronald D

2010-08-01

Fungal and bacterial carbon dioxide (CO2) production/emission was determined under a range of redox conditions in sediment from a Louisiana swamp forest used for wastewater treatment. Sediment was incubated in microcosms at 6 Eh levels (-200, -100, 0, +100, +250 and +400 mV) covering the anaerobic range found in wetland soil and sediment. Carbon dioxide production was determined by the substrate-induced respiration (SIR) inhibition method. Cycloheximide (C15H23NO4) was used as the fungal inhibitor and streptomycin (C21H39N7O12) as the bacterial inhibitor. Under moderately reducing conditions (Eh > +250 mV), fungi contributed more than bacteria to the CO2 production. Under highly reducing conditions (Eh < or = 0 mV), bacteria contributed more than fungi to the total CO2 production. The fungi/bacteria (F/B) ratios varied between 0.71-1.16 for microbial biomass C, and 0.54-0.94 for microbial biomass N. Under moderately reducing conditions (Eh > or = +100 mV), the F/B ratios for microbial biomass C and N were higher than that for highly reducing conditions (Eh < or = 0 mV). In moderately reducing conditions (Eh > or = +100 mV), the C/N microbial biomass ratio for fungi (C/N: 13.54-14.26) was slightly higher than for bacteria (C/N: 9.61-12.07). Under highly reducing redox conditions (Eh < or = 0 mV), the C/N microbial biomass ratio for fungi (C/N: 10.79-12.41) was higher than for bacteria (C/N: 8.21-9.14). For bacteria and fungi, the C/N microbial biomass ratios under moderately reducing conditions were higher than that in highly reducing conditions. Fungal CO2 production from swamp forest could be of greater ecological significance under moderately reducing sediment conditions contributing to the greenhouse effect (GHE) and the global warming potential (GWP). However, increases in coastal submergence associated with global sea level rise and resultant decrease in sediment redox potential from increased flooding would likely shift CO2 production to bacteria rather than

Selective consumption and metabolic allocation of terrestrial and algal carbon determine allochthony in lake bacteria.

PubMed

Guillemette, François; Leigh McCallister, S; Del Giorgio, Paul A

2016-06-01

Here we explore strategies of resource utilization and allocation of algal versus terrestrially derived carbon (C) by lake bacterioplankton. We quantified the consumption of terrestrial and algal dissolved organic carbon, and the subsequent allocation of these pools to bacterial growth and respiration, based on the δ(13)C isotopic signatures of bacterial biomass and respiratory carbon dioxide (CO2). Our results confirm that bacterial communities preferentially remove algal C from the terrestrially dominated organic C pool of lakes, but contrary to current assumptions, selectively allocate this autochthonous substrate to respiration, whereas terrestrial C was preferentially allocated to biosynthesis. The results provide further evidence of a mechanism whereby inputs of labile, algal-derived organic C may stimulate the incorporation of a more recalcitrant, terrestrial C pool. This mechanism resulted in a counterintuitive pattern of high and relatively constant levels of allochthony (~76%) in bacterial biomass across lakes that otherwise differ greatly in productivity and external inputs.

Selective consumption and metabolic allocation of terrestrial and algal carbon determine allochthony in lake bacteria

PubMed Central

Guillemette, François; Leigh McCallister, S; del Giorgio, Paul A

2016-01-01

Here we explore strategies of resource utilization and allocation of algal versus terrestrially derived carbon (C) by lake bacterioplankton. We quantified the consumption of terrestrial and algal dissolved organic carbon, and the subsequent allocation of these pools to bacterial growth and respiration, based on the δ13C isotopic signatures of bacterial biomass and respiratory carbon dioxide (CO2). Our results confirm that bacterial communities preferentially remove algal C from the terrestrially dominated organic C pool of lakes, but contrary to current assumptions, selectively allocate this autochthonous substrate to respiration, whereas terrestrial C was preferentially allocated to biosynthesis. The results provide further evidence of a mechanism whereby inputs of labile, algal-derived organic C may stimulate the incorporation of a more recalcitrant, terrestrial C pool. This mechanism resulted in a counterintuitive pattern of high and relatively constant levels of allochthony (~76%) in bacterial biomass across lakes that otherwise differ greatly in productivity and external inputs. PMID:26623544

O antigen modulates insect vector acquisition of the bacterial plant pathogen Xylella fastidiosa.

PubMed

Rapicavoli, Jeannette N; Kinsinger, Nichola; Perring, Thomas M; Backus, Elaine A; Shugart, Holly J; Walker, Sharon; Roper, M Caroline

2015-12-01

Hemipteran insect vectors transmit the majority of plant pathogens. Acquisition of pathogenic bacteria by these piercing/sucking insects requires intimate associations between the bacterial cells and insect surfaces. Lipopolysaccharide (LPS) is the predominant macromolecule displayed on the cell surface of Gram-negative bacteria and thus mediates bacterial interactions with the environment and potential hosts. We hypothesized that bacterial cell surface properties mediated by LPS would be important in modulating vector-pathogen interactions required for acquisition of the bacterial plant pathogen Xylella fastidiosa, the causative agent of Pierce's disease of grapevines. Utilizing a mutant that produces truncated O antigen (the terminal portion of the LPS molecule), we present results that link this LPS structural alteration to a significant decrease in the attachment of X. fastidiosa to blue-green sharpshooter foreguts. Scanning electron microscopy confirmed that this defect in initial attachment compromised subsequent biofilm formation within vector foreguts, thus impairing pathogen acquisition. We also establish a relationship between O antigen truncation and significant changes in the physiochemical properties of the cell, which in turn affect the dynamics of X. fastidiosa adhesion to the vector foregut. Lastly, we couple measurements of the physiochemical properties of the cell with hydrodynamic fluid shear rates to produce a Comsol model that predicts primary areas of bacterial colonization within blue-green sharpshooter foreguts, and we present experimental data that support the model. These results demonstrate that, in addition to reported protein adhesin-ligand interactions, O antigen is crucial for vector-pathogen interactions, specifically in the acquisition of this destructive agricultural pathogen. Copyright © 2015, American Society for Microbiology. All Rights Reserved.